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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;all_features&quot;,&quot;context&quot;:&quot;product&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;all_features_link_product_navbar&quot;}" href="https://github.com/features">
      All features

    
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary Link--external" target="_blank" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;documentation&quot;,&quot;context&quot;:&quot;product&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;documentation_link_product_navbar&quot;}" href="https://docs.github.com">
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      Blog

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        Solutions
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                    <span class="d-block h4 color-fg-default my-1" id="solutions-by-company-size-heading">By company size</span>
                <ul class="list-style-none f5" aria-labelledby="solutions-by-company-size-heading">
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;enterprises&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;enterprises_link_solutions_navbar&quot;}" href="https://github.com/enterprise">
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;startups&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;startups_link_solutions_navbar&quot;}" href="https://github.com/enterprise/startups">
      Startups

    
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                    <span class="d-block h4 color-fg-default my-1" id="solutions-by-use-case-heading">By use case</span>
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;devops&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;devops_link_solutions_navbar&quot;}" href="/solutions/use-case/devops">
      DevOps

    
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;ci_cd&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;ci_cd_link_solutions_navbar&quot;}" href="/solutions/use-case/ci-cd">
      CI/CD

    
</a></li>

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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;view_all_use_cases&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;view_all_use_cases_link_solutions_navbar&quot;}" href="/solutions/use-case">
      View all use cases

    
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              <div class="border-bottom pb-3 pb-lg-0 border-lg-bottom-0">
                    <span class="d-block h4 color-fg-default my-1" id="solutions-by-industry-heading">By industry</span>
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;healthcare&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;healthcare_link_solutions_navbar&quot;}" href="/solutions/industry/healthcare">
      Healthcare

    
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;financial_services&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;financial_services_link_solutions_navbar&quot;}" href="/solutions/industry/financial-services">
      Financial services

    
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;manufacturing&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;manufacturing_link_solutions_navbar&quot;}" href="/solutions/industry/manufacturing">
      Manufacturing

    
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;government&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;government_link_solutions_navbar&quot;}" href="/solutions/industry/government">
      Government

    
</a></li>

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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;view_all_industries&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;view_all_industries_link_solutions_navbar&quot;}" href="/solutions/industry">
      View all industries

    
</a></li>

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         <div class="HeaderMenu-trailing-link rounded-bottom-2 flex-shrink-0 mt-lg-4 px-lg-4 py-4 py-lg-3 f5 text-semibold">
            <a href="/solutions">
              View all solutions
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        Resources
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                    <span class="d-block h4 color-fg-default my-1" id="resources-topics-heading">Topics</span>
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;ai&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;ai_link_resources_navbar&quot;}" href="/resources/articles/ai">
      AI

    
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;devops&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;devops_link_resources_navbar&quot;}" href="/resources/articles/devops">
      DevOps

    
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;security&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;security_link_resources_navbar&quot;}" href="/resources/articles/security">
      Security

    
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;software_development&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;software_development_link_resources_navbar&quot;}" href="/resources/articles/software-development">
      Software Development

    
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;view_all&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;view_all_link_resources_navbar&quot;}" href="/resources/articles">
      View all

    
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                    <span class="d-block h4 color-fg-default my-1" id="resources-explore-heading">Explore</span>
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary Link--external" target="_blank" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;learning_pathways&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;learning_pathways_link_resources_navbar&quot;}" href="https://resources.github.com/learn/pathways">
      Learning Pathways

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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary Link--external" target="_blank" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;white_papers_ebooks_webinars&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;white_papers_ebooks_webinars_link_resources_navbar&quot;}" href="https://resources.github.com">
      White papers, Ebooks, Webinars

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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;customer_stories&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;customer_stories_link_resources_navbar&quot;}" href="https://github.com/customer-stories">
      Customer Stories

    
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary Link--external" target="_blank" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;partners&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;partners_link_resources_navbar&quot;}" href="https://partner.github.com">
      Partners

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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;executive_insights&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;executive_insights_link_resources_navbar&quot;}" href="https://github.com/solutions/executive-insights">
      Executive Insights

    
</a></li>

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          </div>
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</li>


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        Open Source
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;github_sponsors&quot;,&quot;context&quot;:&quot;open_source&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;github_sponsors_link_open_source_navbar&quot;}" href="/sponsors">
      
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        Fund open source developers
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</a></li>

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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;the_readme_project&quot;,&quot;context&quot;:&quot;open_source&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;the_readme_project_link_open_source_navbar&quot;}" href="https://github.com/readme">
      
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                    <span class="d-block h4 color-fg-default my-1" id="open-source-repositories-heading">Repositories</span>
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;topics&quot;,&quot;context&quot;:&quot;open_source&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;topics_link_open_source_navbar&quot;}" href="https://github.com/topics">
      Topics

    
</a></li>

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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;trending&quot;,&quot;context&quot;:&quot;open_source&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;trending_link_open_source_navbar&quot;}" href="https://github.com/trending">
      Trending

    
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;collections&quot;,&quot;context&quot;:&quot;open_source&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;collections_link_open_source_navbar&quot;}" href="https://github.com/collections">
      Collections

    
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          </div>
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</li>


                <li class="HeaderMenu-item position-relative flex-wrap flex-justify-between flex-items-center d-block d-lg-flex flex-lg-nowrap flex-lg-items-center js-details-container js-header-menu-item">
      <button type="button" class="HeaderMenu-link border-0 width-full width-lg-auto px-0 px-lg-2 py-lg-2 no-wrap d-flex flex-items-center flex-justify-between js-details-target" aria-expanded="false">
        Enterprise
        <svg opacity="0.5" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-chevron-down HeaderMenu-icon ml-1">
    <path d="M12.78 5.22a.749.749 0 0 1 0 1.06l-4.25 4.25a.749.749 0 0 1-1.06 0L3.22 6.28a.749.749 0 1 1 1.06-1.06L8 8.939l3.72-3.719a.749.749 0 0 1 1.06 0Z"></path>
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      </button>
      <div class="HeaderMenu-dropdown dropdown-menu rounded m-0 p-0 pt-2 pt-lg-4 position-relative position-lg-absolute left-0 left-lg-n3 pb-2 pb-lg-4 px-lg-4">
          <div class="HeaderMenu-column">
              <div class="border-bottom pb-3 pb-lg-0 pb-lg-3 mb-3 mb-lg-0 mb-lg-3">
                <ul class="list-style-none f5" >
                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;enterprise_platform&quot;,&quot;context&quot;:&quot;enterprise&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;enterprise_platform_link_enterprise_navbar&quot;}" href="/enterprise">
      <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-stack color-fg-subtle mr-3">
    <path d="M11.063 1.456a1.749 1.749 0 0 1 1.874 0l8.383 5.316a1.751 1.751 0 0 1 0 2.956l-8.383 5.316a1.749 1.749 0 0 1-1.874 0L2.68 9.728a1.751 1.751 0 0 1 0-2.956Zm1.071 1.267a.25.25 0 0 0-.268 0L3.483 8.039a.25.25 0 0 0 0 .422l8.383 5.316a.25.25 0 0 0 .268 0l8.383-5.316a.25.25 0 0 0 0-.422Z"></path><path d="M1.867 12.324a.75.75 0 0 1 1.035-.232l8.964 5.685a.25.25 0 0 0 .268 0l8.964-5.685a.75.75 0 0 1 .804 1.267l-8.965 5.685a1.749 1.749 0 0 1-1.874 0l-8.965-5.685a.75.75 0 0 1-.231-1.035Z"></path><path d="M1.867 16.324a.75.75 0 0 1 1.035-.232l8.964 5.685a.25.25 0 0 0 .268 0l8.964-5.685a.75.75 0 0 1 .804 1.267l-8.965 5.685a1.749 1.749 0 0 1-1.874 0l-8.965-5.685a.75.75 0 0 1-.231-1.035Z"></path>
</svg>
      <div>
        <div class="color-fg-default h4">Enterprise platform</div>
        AI-powered developer platform
      </div>

    
</a></li>

                </ul>
              </div>
              <div class="border-bottom pb-3 pb-lg-0 border-bottom-0">
                    <span class="d-block h4 color-fg-default my-1" id="enterprise-available-add-ons-heading">Available add-ons</span>
                <ul class="list-style-none f5" aria-labelledby="enterprise-available-add-ons-heading">
                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;advanced_security&quot;,&quot;context&quot;:&quot;enterprise&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;advanced_security_link_enterprise_navbar&quot;}" href="https://github.com/enterprise/advanced-security">
      <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-shield-check color-fg-subtle mr-3">
    <path d="M16.53 9.78a.75.75 0 0 0-1.06-1.06L11 13.19l-1.97-1.97a.75.75 0 0 0-1.06 1.06l2.5 2.5a.75.75 0 0 0 1.06 0l5-5Z"></path><path d="m12.54.637 8.25 2.675A1.75 1.75 0 0 1 22 4.976V10c0 6.19-3.771 10.704-9.401 12.83a1.704 1.704 0 0 1-1.198 0C5.77 20.705 2 16.19 2 10V4.976c0-.758.489-1.43 1.21-1.664L11.46.637a1.748 1.748 0 0 1 1.08 0Zm-.617 1.426-8.25 2.676a.249.249 0 0 0-.173.237V10c0 5.46 3.28 9.483 8.43 11.426a.199.199 0 0 0 .14 0C17.22 19.483 20.5 15.461 20.5 10V4.976a.25.25 0 0 0-.173-.237l-8.25-2.676a.253.253 0 0 0-.154 0Z"></path>
</svg>
      <div>
        <div class="color-fg-default h4">Advanced Security</div>
        Enterprise-grade security features
      </div>

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;github_copilot&quot;,&quot;context&quot;:&quot;enterprise&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;github_copilot_link_enterprise_navbar&quot;}" href="/features/copilot#enterprise">
      <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-copilot color-fg-subtle mr-3">
    <path d="M23.922 16.992c-.861 1.495-5.859 5.023-11.922 5.023-6.063 0-11.061-3.528-11.922-5.023A.641.641 0 0 1 0 16.736v-2.869a.841.841 0 0 1 .053-.22c.372-.935 1.347-2.292 2.605-2.656.167-.429.414-1.055.644-1.517a10.195 10.195 0 0 1-.052-1.086c0-1.331.282-2.499 1.132-3.368.397-.406.89-.717 1.474-.952 1.399-1.136 3.392-2.093 6.122-2.093 2.731 0 4.767.957 6.166 2.093.584.235 1.077.546 1.474.952.85.869 1.132 2.037 1.132 3.368 0 .368-.014.733-.052 1.086.23.462.477 1.088.644 1.517 1.258.364 2.233 1.721 2.605 2.656a.832.832 0 0 1 .053.22v2.869a.641.641 0 0 1-.078.256ZM12.172 11h-.344a4.323 4.323 0 0 1-.355.508C10.703 12.455 9.555 13 7.965 13c-1.725 0-2.989-.359-3.782-1.259a2.005 2.005 0 0 1-.085-.104L4 11.741v6.585c1.435.779 4.514 2.179 8 2.179 3.486 0 6.565-1.4 8-2.179v-6.585l-.098-.104s-.033.045-.085.104c-.793.9-2.057 1.259-3.782 1.259-1.59 0-2.738-.545-3.508-1.492a4.323 4.323 0 0 1-.355-.508h-.016.016Zm.641-2.935c.136 1.057.403 1.913.878 2.497.442.544 1.134.938 2.344.938 1.573 0 2.292-.337 2.657-.751.384-.435.558-1.15.558-2.361 0-1.14-.243-1.847-.705-2.319-.477-.488-1.319-.862-2.824-1.025-1.487-.161-2.192.138-2.533.529-.269.307-.437.808-.438 1.578v.021c0 .265.021.562.063.893Zm-1.626 0c.042-.331.063-.628.063-.894v-.02c-.001-.77-.169-1.271-.438-1.578-.341-.391-1.046-.69-2.533-.529-1.505.163-2.347.537-2.824 1.025-.462.472-.705 1.179-.705 2.319 0 1.211.175 1.926.558 2.361.365.414 1.084.751 2.657.751 1.21 0 1.902-.394 2.344-.938.475-.584.742-1.44.878-2.497Z"></path><path d="M14.5 14.25a1 1 0 0 1 1 1v2a1 1 0 0 1-2 0v-2a1 1 0 0 1 1-1Zm-5 0a1 1 0 0 1 1 1v2a1 1 0 0 1-2 0v-2a1 1 0 0 1 1-1Z"></path>
</svg>
      <div>
        <div class="color-fg-default h4">GitHub Copilot</div>
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</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;premium_support&quot;,&quot;context&quot;:&quot;enterprise&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;premium_support_link_enterprise_navbar&quot;}" href="/premium-support">
      <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-comment-discussion color-fg-subtle mr-3">
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</svg>
      <div>
        <div class="color-fg-default h4">Premium Support</div>
        Enterprise-grade 24/7 support
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</a></li>

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</li>


                <li class="HeaderMenu-item position-relative flex-wrap flex-justify-between flex-items-center d-block d-lg-flex flex-lg-nowrap flex-lg-items-center js-details-container js-header-menu-item">
    <a class="HeaderMenu-link no-underline px-0 px-lg-2 py-3 py-lg-2 d-block d-lg-inline-block" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;pricing&quot;,&quot;context&quot;:&quot;global&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;pricing_link_global_navbar&quot;}" href="https://github.com/pricing">Pricing</a>
</li>

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          </nav>

        <div class="d-flex flex-column flex-lg-row width-full flex-justify-end flex-lg-items-center text-center mt-3 mt-lg-0 text-lg-left ml-lg-3">
                


<qbsearch-input class="search-input" data-scope="repo:instanseg/instanseg" data-custom-scopes-path="/search/custom_scopes" data-delete-custom-scopes-csrf="EuQtjksAn_oJkp6Xl8q5vY9SVMGpEhPW9fw9u7klxuB27tS6F-023mRaPO1-biEggy4mCyw_E53TeH2-LTVKCQ" data-max-custom-scopes="10" data-header-redesign-enabled="false" data-initial-value="" data-blackbird-suggestions-path="/search/suggestions" data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations" data-current-repository="instanseg/instanseg" data-current-org="instanseg" data-current-owner="" data-logged-in="false" data-copilot-chat-enabled="false" data-nl-search-enabled="false" data-retain-scroll-position="true">
  <div
    class="search-input-container search-with-dialog position-relative d-flex flex-row flex-items-center mr-4 rounded"
    data-action="click:qbsearch-input#searchInputContainerClicked"
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      <button
        type="button"
        class="header-search-button placeholder  input-button form-control d-flex flex-1 flex-self-stretch flex-items-center no-wrap width-full py-0 pl-2 pr-0 text-left border-0 box-shadow-none"
        data-target="qbsearch-input.inputButton"
        aria-label="Search or jump to…"
        aria-haspopup="dialog"
        placeholder="Search or jump to..."
        data-hotkey=s,/
        autocapitalize="off"
        data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;searchbar&quot;,&quot;context&quot;:&quot;global&quot;,&quot;tag&quot;:&quot;input&quot;,&quot;label&quot;:&quot;searchbar_input_global_navbar&quot;}"
        data-action="click:qbsearch-input#handleExpand"
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        <div class="mr-2 color-fg-muted">
          <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-search">
    <path d="M10.68 11.74a6 6 0 0 1-7.922-8.982 6 6 0 0 1 8.982 7.922l3.04 3.04a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215ZM11.5 7a4.499 4.499 0 1 0-8.997 0A4.499 4.499 0 0 0 11.5 7Z"></path>
</svg>
        </div>
        <span class="flex-1" data-target="qbsearch-input.inputButtonText">Search or jump to...</span>
          <div class="d-flex" data-target="qbsearch-input.hotkeyIndicator">
            <svg xmlns="http://www.w3.org/2000/svg" width="22" height="20" aria-hidden="true" class="mr-1"><path fill="none" stroke="#979A9C" opacity=".4" d="M3.5.5h12c1.7 0 3 1.3 3 3v13c0 1.7-1.3 3-3 3h-12c-1.7 0-3-1.3-3-3v-13c0-1.7 1.3-3 3-3z"></path><path fill="#979A9C" d="M11.8 6L8 15.1h-.9L10.8 6h1z"></path></svg>

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    <input type="hidden" name="type" class="js-site-search-type-field">

    
<div class="Overlay--hidden " data-modal-dialog-overlay>
  <modal-dialog data-action="close:qbsearch-input#handleClose cancel:qbsearch-input#handleClose" data-target="qbsearch-input.searchSuggestionsDialog" role="dialog" id="search-suggestions-dialog" aria-modal="true" aria-labelledby="search-suggestions-dialog-header" data-view-component="true" class="Overlay Overlay--width-large Overlay--height-auto">
      <h1 id="search-suggestions-dialog-header" class="sr-only">Search code, repositories, users, issues, pull requests...</h1>
    <div class="Overlay-body Overlay-body--paddingNone">
      
          <div data-view-component="true">        <div class="search-suggestions position-fixed width-full color-shadow-large border color-fg-default color-bg-default overflow-hidden d-flex flex-column query-builder-container"
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          <!-- '"` --><!-- </textarea></xmp> --></option></form><form id="query-builder-test-form" action="" accept-charset="UTF-8" method="get">
  <query-builder data-target="qbsearch-input.queryBuilder" id="query-builder-query-builder-test" data-filter-key=":" data-view-component="true" class="QueryBuilder search-query-builder">
    <div class="FormControl FormControl--fullWidth">
      <label id="query-builder-test-label" for="query-builder-test" class="FormControl-label sr-only">
        Search
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      <div
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        data-target="query-builder.styledInput"
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          <span id="query-builder-test-leadingvisual-wrap" class="FormControl-input-leadingVisualWrap QueryBuilder-leadingVisualWrap">
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    <path d="M10.68 11.74a6 6 0 0 1-7.922-8.982 6 6 0 0 1 8.982 7.922l3.04 3.04a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215ZM11.5 7a4.499 4.499 0 1 0-8.997 0A4.499 4.499 0 0 0 11.5 7Z"></path>
</svg>
          </span>
        <div data-target="query-builder.styledInputContainer" class="QueryBuilder-StyledInputContainer">
          <div
            aria-hidden="true"
            class="QueryBuilder-StyledInputContent"
            data-target="query-builder.styledInputContent"
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          <div class="QueryBuilder-InputWrapper">
            <div aria-hidden="true" class="QueryBuilder-Sizer" data-target="query-builder.sizer"></div>
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          input:query-builder#inputChange
          blur:query-builder#inputBlur
          keydown:query-builder#inputKeydown
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        </div>
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</button>

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      <template id="search-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-search">
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</svg>
</template>

<template id="code-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-code">
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</svg>
</template>

<template id="file-code-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-file-code">
    <path d="M4 1.75C4 .784 4.784 0 5.75 0h5.586c.464 0 .909.184 1.237.513l2.914 2.914c.329.328.513.773.513 1.237v8.586A1.75 1.75 0 0 1 14.25 15h-9a.75.75 0 0 1 0-1.5h9a.25.25 0 0 0 .25-.25V6h-2.75A1.75 1.75 0 0 1 10 4.25V1.5H5.75a.25.25 0 0 0-.25.25v2.5a.75.75 0 0 1-1.5 0Zm1.72 4.97a.75.75 0 0 1 1.06 0l2 2a.75.75 0 0 1 0 1.06l-2 2a.749.749 0 0 1-1.275-.326.749.749 0 0 1 .215-.734l1.47-1.47-1.47-1.47a.75.75 0 0 1 0-1.06ZM3.28 7.78 1.81 9.25l1.47 1.47a.751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018l-2-2a.75.75 0 0 1 0-1.06l2-2a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042Zm8.22-6.218V4.25c0 .138.112.25.25.25h2.688l-.011-.013-2.914-2.914-.013-.011Z"></path>
</svg>
</template>

<template id="history-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-history">
    <path d="m.427 1.927 1.215 1.215a8.002 8.002 0 1 1-1.6 5.685.75.75 0 1 1 1.493-.154 6.5 6.5 0 1 0 1.18-4.458l1.358 1.358A.25.25 0 0 1 3.896 6H.25A.25.25 0 0 1 0 5.75V2.104a.25.25 0 0 1 .427-.177ZM7.75 4a.75.75 0 0 1 .75.75v2.992l2.028.812a.75.75 0 0 1-.557 1.392l-2.5-1A.751.751 0 0 1 7 8.25v-3.5A.75.75 0 0 1 7.75 4Z"></path>
</svg>
</template>

<template id="repo-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-repo">
    <path d="M2 2.5A2.5 2.5 0 0 1 4.5 0h8.75a.75.75 0 0 1 .75.75v12.5a.75.75 0 0 1-.75.75h-2.5a.75.75 0 0 1 0-1.5h1.75v-2h-8a1 1 0 0 0-.714 1.7.75.75 0 1 1-1.072 1.05A2.495 2.495 0 0 1 2 11.5Zm10.5-1h-8a1 1 0 0 0-1 1v6.708A2.486 2.486 0 0 1 4.5 9h8ZM5 12.25a.25.25 0 0 1 .25-.25h3.5a.25.25 0 0 1 .25.25v3.25a.25.25 0 0 1-.4.2l-1.45-1.087a.249.249 0 0 0-.3 0L5.4 15.7a.25.25 0 0 1-.4-.2Z"></path>
</svg>
</template>

<template id="bookmark-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-bookmark">
    <path d="M3 2.75C3 1.784 3.784 1 4.75 1h6.5c.966 0 1.75.784 1.75 1.75v11.5a.75.75 0 0 1-1.227.579L8 11.722l-3.773 3.107A.751.751 0 0 1 3 14.25Zm1.75-.25a.25.25 0 0 0-.25.25v9.91l3.023-2.489a.75.75 0 0 1 .954 0l3.023 2.49V2.75a.25.25 0 0 0-.25-.25Z"></path>
</svg>
</template>

<template id="plus-circle-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-plus-circle">
    <path d="M8 0a8 8 0 1 1 0 16A8 8 0 0 1 8 0ZM1.5 8a6.5 6.5 0 1 0 13 0 6.5 6.5 0 0 0-13 0Zm7.25-3.25v2.5h2.5a.75.75 0 0 1 0 1.5h-2.5v2.5a.75.75 0 0 1-1.5 0v-2.5h-2.5a.75.75 0 0 1 0-1.5h2.5v-2.5a.75.75 0 0 1 1.5 0Z"></path>
</svg>
</template>

<template id="circle-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-dot-fill">
    <path d="M8 4a4 4 0 1 1 0 8 4 4 0 0 1 0-8Z"></path>
</svg>
</template>

<template id="trash-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-trash">
    <path d="M11 1.75V3h2.25a.75.75 0 0 1 0 1.5H2.75a.75.75 0 0 1 0-1.5H5V1.75C5 .784 5.784 0 6.75 0h2.5C10.216 0 11 .784 11 1.75ZM4.496 6.675l.66 6.6a.25.25 0 0 0 .249.225h5.19a.25.25 0 0 0 .249-.225l.66-6.6a.75.75 0 0 1 1.492.149l-.66 6.6A1.748 1.748 0 0 1 10.595 15h-5.19a1.75 1.75 0 0 1-1.741-1.575l-.66-6.6a.75.75 0 1 1 1.492-.15ZM6.5 1.75V3h3V1.75a.25.25 0 0 0-.25-.25h-2.5a.25.25 0 0 0-.25.25Z"></path>
</svg>
</template>

<template id="team-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-people">
    <path d="M2 5.5a3.5 3.5 0 1 1 5.898 2.549 5.508 5.508 0 0 1 3.034 4.084.75.75 0 1 1-1.482.235 4 4 0 0 0-7.9 0 .75.75 0 0 1-1.482-.236A5.507 5.507 0 0 1 3.102 8.05 3.493 3.493 0 0 1 2 5.5ZM11 4a3.001 3.001 0 0 1 2.22 5.018 5.01 5.01 0 0 1 2.56 3.012.749.749 0 0 1-.885.954.752.752 0 0 1-.549-.514 3.507 3.507 0 0 0-2.522-2.372.75.75 0 0 1-.574-.73v-.352a.75.75 0 0 1 .416-.672A1.5 1.5 0 0 0 11 5.5.75.75 0 0 1 11 4Zm-5.5-.5a2 2 0 1 0-.001 3.999A2 2 0 0 0 5.5 3.5Z"></path>
</svg>
</template>

<template id="project-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-project">
    <path d="M1.75 0h12.5C15.216 0 16 .784 16 1.75v12.5A1.75 1.75 0 0 1 14.25 16H1.75A1.75 1.75 0 0 1 0 14.25V1.75C0 .784.784 0 1.75 0ZM1.5 1.75v12.5c0 .138.112.25.25.25h12.5a.25.25 0 0 0 .25-.25V1.75a.25.25 0 0 0-.25-.25H1.75a.25.25 0 0 0-.25.25ZM11.75 3a.75.75 0 0 1 .75.75v7.5a.75.75 0 0 1-1.5 0v-7.5a.75.75 0 0 1 .75-.75Zm-8.25.75a.75.75 0 0 1 1.5 0v5.5a.75.75 0 0 1-1.5 0ZM8 3a.75.75 0 0 1 .75.75v3.5a.75.75 0 0 1-1.5 0v-3.5A.75.75 0 0 1 8 3Z"></path>
</svg>
</template>

<template id="pencil-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-pencil">
    <path d="M11.013 1.427a1.75 1.75 0 0 1 2.474 0l1.086 1.086a1.75 1.75 0 0 1 0 2.474l-8.61 8.61c-.21.21-.47.364-.756.445l-3.251.93a.75.75 0 0 1-.927-.928l.929-3.25c.081-.286.235-.547.445-.758l8.61-8.61Zm.176 4.823L9.75 4.81l-6.286 6.287a.253.253 0 0 0-.064.108l-.558 1.953 1.953-.558a.253.253 0 0 0 .108-.064Zm1.238-3.763a.25.25 0 0 0-.354 0L10.811 3.75l1.439 1.44 1.263-1.263a.25.25 0 0 0 0-.354Z"></path>
</svg>
</template>

<template id="copilot-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copilot">
    <path d="M7.998 15.035c-4.562 0-7.873-2.914-7.998-3.749V9.338c.085-.628.677-1.686 1.588-2.065.013-.07.024-.143.036-.218.029-.183.06-.384.126-.612-.201-.508-.254-1.084-.254-1.656 0-.87.128-1.769.693-2.484.579-.733 1.494-1.124 2.724-1.261 1.206-.134 2.262.034 2.944.765.05.053.096.108.139.165.044-.057.094-.112.143-.165.682-.731 1.738-.899 2.944-.765 1.23.137 2.145.528 2.724 1.261.566.715.693 1.614.693 2.484 0 .572-.053 1.148-.254 1.656.066.228.098.429.126.612.012.076.024.148.037.218.924.385 1.522 1.471 1.591 2.095v1.872c0 .766-3.351 3.795-8.002 3.795Zm0-1.485c2.28 0 4.584-1.11 5.002-1.433V7.862l-.023-.116c-.49.21-1.075.291-1.727.291-1.146 0-2.059-.327-2.71-.991A3.222 3.222 0 0 1 8 6.303a3.24 3.24 0 0 1-.544.743c-.65.664-1.563.991-2.71.991-.652 0-1.236-.081-1.727-.291l-.023.116v4.255c.419.323 2.722 1.433 5.002 1.433ZM6.762 2.83c-.193-.206-.637-.413-1.682-.297-1.019.113-1.479.404-1.713.7-.247.312-.369.789-.369 1.554 0 .793.129 1.171.308 1.371.162.181.519.379 1.442.379.853 0 1.339-.235 1.638-.54.315-.322.527-.827.617-1.553.117-.935-.037-1.395-.241-1.614Zm4.155-.297c-1.044-.116-1.488.091-1.681.297-.204.219-.359.679-.242 1.614.091.726.303 1.231.618 1.553.299.305.784.54 1.638.54.922 0 1.28-.198 1.442-.379.179-.2.308-.578.308-1.371 0-.765-.123-1.242-.37-1.554-.233-.296-.693-.587-1.713-.7Z"></path><path d="M6.25 9.037a.75.75 0 0 1 .75.75v1.501a.75.75 0 0 1-1.5 0V9.787a.75.75 0 0 1 .75-.75Zm4.25.75v1.501a.75.75 0 0 1-1.5 0V9.787a.75.75 0 0 1 1.5 0Z"></path>
</svg>
</template>

<template id="copilot-error-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copilot-error">
    <path d="M16 11.24c0 .112-.072.274-.21.467L13 9.688V7.862l-.023-.116c-.49.21-1.075.291-1.727.291-.198 0-.388-.009-.571-.029L6.833 5.226a4.01 4.01 0 0 0 .17-.782c.117-.935-.037-1.395-.241-1.614-.193-.206-.637-.413-1.682-.297-.683.076-1.115.231-1.395.415l-1.257-.91c.579-.564 1.413-.877 2.485-.996 1.206-.134 2.262.034 2.944.765.05.053.096.108.139.165.044-.057.094-.112.143-.165.682-.731 1.738-.899 2.944-.765 1.23.137 2.145.528 2.724 1.261.566.715.693 1.614.693 2.484 0 .572-.053 1.148-.254 1.656.066.228.098.429.126.612.012.076.024.148.037.218.924.385 1.522 1.471 1.591 2.095Zm-5.083-8.707c-1.044-.116-1.488.091-1.681.297-.204.219-.359.679-.242 1.614.091.726.303 1.231.618 1.553.299.305.784.54 1.638.54.922 0 1.28-.198 1.442-.379.179-.2.308-.578.308-1.371 0-.765-.123-1.242-.37-1.554-.233-.296-.693-.587-1.713-.7Zm2.511 11.074c-1.393.776-3.272 1.428-5.43 1.428-4.562 0-7.873-2.914-7.998-3.749V9.338c.085-.628.677-1.686 1.588-2.065.013-.07.024-.143.036-.218.029-.183.06-.384.126-.612-.18-.455-.241-.963-.252-1.475L.31 4.107A.747.747 0 0 1 0 3.509V3.49a.748.748 0 0 1 .625-.73c.156-.026.306.047.435.139l14.667 10.578a.592.592 0 0 1 .227.264.752.752 0 0 1 .046.249v.022a.75.75 0 0 1-1.19.596Zm-1.367-.991L5.635 7.964a5.128 5.128 0 0 1-.889.073c-.652 0-1.236-.081-1.727-.291l-.023.116v4.255c.419.323 2.722 1.433 5.002 1.433 1.539 0 3.089-.505 4.063-.934Z"></path>
</svg>
</template>

<template id="workflow-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-workflow">
    <path d="M0 1.75C0 .784.784 0 1.75 0h3.5C6.216 0 7 .784 7 1.75v3.5A1.75 1.75 0 0 1 5.25 7H4v4a1 1 0 0 0 1 1h4v-1.25C9 9.784 9.784 9 10.75 9h3.5c.966 0 1.75.784 1.75 1.75v3.5A1.75 1.75 0 0 1 14.25 16h-3.5A1.75 1.75 0 0 1 9 14.25v-.75H5A2.5 2.5 0 0 1 2.5 11V7h-.75A1.75 1.75 0 0 1 0 5.25Zm1.75-.25a.25.25 0 0 0-.25.25v3.5c0 .138.112.25.25.25h3.5a.25.25 0 0 0 .25-.25v-3.5a.25.25 0 0 0-.25-.25Zm9 9a.25.25 0 0 0-.25.25v3.5c0 .138.112.25.25.25h3.5a.25.25 0 0 0 .25-.25v-3.5a.25.25 0 0 0-.25-.25Z"></path>
</svg>
</template>

<template id="book-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-book">
    <path d="M0 1.75A.75.75 0 0 1 .75 1h4.253c1.227 0 2.317.59 3 1.501A3.743 3.743 0 0 1 11.006 1h4.245a.75.75 0 0 1 .75.75v10.5a.75.75 0 0 1-.75.75h-4.507a2.25 2.25 0 0 0-1.591.659l-.622.621a.75.75 0 0 1-1.06 0l-.622-.621A2.25 2.25 0 0 0 5.258 13H.75a.75.75 0 0 1-.75-.75Zm7.251 10.324.004-5.073-.002-2.253A2.25 2.25 0 0 0 5.003 2.5H1.5v9h3.757a3.75 3.75 0 0 1 1.994.574ZM8.755 4.75l-.004 7.322a3.752 3.752 0 0 1 1.992-.572H14.5v-9h-3.495a2.25 2.25 0 0 0-2.25 2.25Z"></path>
</svg>
</template>

<template id="code-review-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-code-review">
    <path d="M1.75 1h12.5c.966 0 1.75.784 1.75 1.75v8.5A1.75 1.75 0 0 1 14.25 13H8.061l-2.574 2.573A1.458 1.458 0 0 1 3 14.543V13H1.75A1.75 1.75 0 0 1 0 11.25v-8.5C0 1.784.784 1 1.75 1ZM1.5 2.75v8.5c0 .138.112.25.25.25h2a.75.75 0 0 1 .75.75v2.19l2.72-2.72a.749.749 0 0 1 .53-.22h6.5a.25.25 0 0 0 .25-.25v-8.5a.25.25 0 0 0-.25-.25H1.75a.25.25 0 0 0-.25.25Zm5.28 1.72a.75.75 0 0 1 0 1.06L5.31 7l1.47 1.47a.751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018l-2-2a.75.75 0 0 1 0-1.06l2-2a.75.75 0 0 1 1.06 0Zm2.44 0a.75.75 0 0 1 1.06 0l2 2a.75.75 0 0 1 0 1.06l-2 2a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L10.69 7 9.22 5.53a.75.75 0 0 1 0-1.06Z"></path>
</svg>
</template>

<template id="codespaces-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-codespaces">
    <path d="M0 11.25c0-.966.784-1.75 1.75-1.75h12.5c.966 0 1.75.784 1.75 1.75v3A1.75 1.75 0 0 1 14.25 16H1.75A1.75 1.75 0 0 1 0 14.25Zm2-9.5C2 .784 2.784 0 3.75 0h8.5C13.216 0 14 .784 14 1.75v5a1.75 1.75 0 0 1-1.75 1.75h-8.5A1.75 1.75 0 0 1 2 6.75Zm1.75-.25a.25.25 0 0 0-.25.25v5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-5a.25.25 0 0 0-.25-.25Zm-2 9.5a.25.25 0 0 0-.25.25v3c0 .138.112.25.25.25h12.5a.25.25 0 0 0 .25-.25v-3a.25.25 0 0 0-.25-.25Z"></path><path d="M7 12.75a.75.75 0 0 1 .75-.75h4.5a.75.75 0 0 1 0 1.5h-4.5a.75.75 0 0 1-.75-.75Zm-4 0a.75.75 0 0 1 .75-.75h.5a.75.75 0 0 1 0 1.5h-.5a.75.75 0 0 1-.75-.75Z"></path>
</svg>
</template>

<template id="comment-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-comment">
    <path d="M1 2.75C1 1.784 1.784 1 2.75 1h10.5c.966 0 1.75.784 1.75 1.75v7.5A1.75 1.75 0 0 1 13.25 12H9.06l-2.573 2.573A1.458 1.458 0 0 1 4 13.543V12H2.75A1.75 1.75 0 0 1 1 10.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h2a.75.75 0 0 1 .75.75v2.19l2.72-2.72a.749.749 0 0 1 .53-.22h4.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path>
</svg>
</template>

<template id="comment-discussion-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-comment-discussion">
    <path d="M1.75 1h8.5c.966 0 1.75.784 1.75 1.75v5.5A1.75 1.75 0 0 1 10.25 10H7.061l-2.574 2.573A1.458 1.458 0 0 1 2 11.543V10h-.25A1.75 1.75 0 0 1 0 8.25v-5.5C0 1.784.784 1 1.75 1ZM1.5 2.75v5.5c0 .138.112.25.25.25h1a.75.75 0 0 1 .75.75v2.19l2.72-2.72a.749.749 0 0 1 .53-.22h3.5a.25.25 0 0 0 .25-.25v-5.5a.25.25 0 0 0-.25-.25h-8.5a.25.25 0 0 0-.25.25Zm13 2a.25.25 0 0 0-.25-.25h-.5a.75.75 0 0 1 0-1.5h.5c.966 0 1.75.784 1.75 1.75v5.5A1.75 1.75 0 0 1 14.25 12H14v1.543a1.458 1.458 0 0 1-2.487 1.03L9.22 12.28a.749.749 0 0 1 .326-1.275.749.749 0 0 1 .734.215l2.22 2.22v-2.19a.75.75 0 0 1 .75-.75h1a.25.25 0 0 0 .25-.25Z"></path>
</svg>
</template>

<template id="organization-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-organization">
    <path d="M1.75 16A1.75 1.75 0 0 1 0 14.25V1.75C0 .784.784 0 1.75 0h8.5C11.216 0 12 .784 12 1.75v12.5c0 .085-.006.168-.018.25h2.268a.25.25 0 0 0 .25-.25V8.285a.25.25 0 0 0-.111-.208l-1.055-.703a.749.749 0 1 1 .832-1.248l1.055.703c.487.325.779.871.779 1.456v5.965A1.75 1.75 0 0 1 14.25 16h-3.5a.766.766 0 0 1-.197-.026c-.099.017-.2.026-.303.026h-3a.75.75 0 0 1-.75-.75V14h-1v1.25a.75.75 0 0 1-.75.75Zm-.25-1.75c0 .138.112.25.25.25H4v-1.25a.75.75 0 0 1 .75-.75h2.5a.75.75 0 0 1 .75.75v1.25h2.25a.25.25 0 0 0 .25-.25V1.75a.25.25 0 0 0-.25-.25h-8.5a.25.25 0 0 0-.25.25ZM3.75 6h.5a.75.75 0 0 1 0 1.5h-.5a.75.75 0 0 1 0-1.5ZM3 3.75A.75.75 0 0 1 3.75 3h.5a.75.75 0 0 1 0 1.5h-.5A.75.75 0 0 1 3 3.75Zm4 3A.75.75 0 0 1 7.75 6h.5a.75.75 0 0 1 0 1.5h-.5A.75.75 0 0 1 7 6.75ZM7.75 3h.5a.75.75 0 0 1 0 1.5h-.5a.75.75 0 0 1 0-1.5ZM3 9.75A.75.75 0 0 1 3.75 9h.5a.75.75 0 0 1 0 1.5h-.5A.75.75 0 0 1 3 9.75ZM7.75 9h.5a.75.75 0 0 1 0 1.5h-.5a.75.75 0 0 1 0-1.5Z"></path>
</svg>
</template>

<template id="rocket-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-rocket">
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<template id="shield-check-icon">
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<template id="heart-icon">
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<template id="server-icon">
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<template id="globe-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-globe">
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<template id="issue-opened-icon">
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<template id="device-mobile-icon">
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<template id="package-icon">
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<template id="credit-card-icon">
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    <path d="M10.75 9a.75.75 0 0 0 0 1.5h1.5a.75.75 0 0 0 0-1.5h-1.5Z"></path><path d="M0 3.75C0 2.784.784 2 1.75 2h12.5c.966 0 1.75.784 1.75 1.75v8.5A1.75 1.75 0 0 1 14.25 14H1.75A1.75 1.75 0 0 1 0 12.25ZM14.5 6.5h-13v5.75c0 .138.112.25.25.25h12.5a.25.25 0 0 0 .25-.25Zm0-2.75a.25.25 0 0 0-.25-.25H1.75a.25.25 0 0 0-.25.25V5h13Z"></path>
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<template id="play-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-play">
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<template id="gift-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-gift">
    <path d="M2 2.75A2.75 2.75 0 0 1 4.75 0c.983 0 1.873.42 2.57 1.232.268.318.497.668.68 1.042.183-.375.411-.725.68-1.044C9.376.42 10.266 0 11.25 0a2.75 2.75 0 0 1 2.45 4h.55c.966 0 1.75.784 1.75 1.75v2c0 .698-.409 1.301-1 1.582v4.918A1.75 1.75 0 0 1 13.25 16H2.75A1.75 1.75 0 0 1 1 14.25V9.332C.409 9.05 0 8.448 0 7.75v-2C0 4.784.784 4 1.75 4h.55c-.192-.375-.3-.8-.3-1.25ZM7.25 9.5H2.5v4.75c0 .138.112.25.25.25h4.5Zm1.5 0v5h4.5a.25.25 0 0 0 .25-.25V9.5Zm0-4V8h5.5a.25.25 0 0 0 .25-.25v-2a.25.25 0 0 0-.25-.25Zm-7 0a.25.25 0 0 0-.25.25v2c0 .138.112.25.25.25h5.5V5.5h-5.5Zm3-4a1.25 1.25 0 0 0 0 2.5h2.309c-.233-.818-.542-1.401-.878-1.793-.43-.502-.915-.707-1.431-.707ZM8.941 4h2.309a1.25 1.25 0 0 0 0-2.5c-.516 0-1 .205-1.43.707-.337.392-.646.975-.879 1.793Z"></path>
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<template id="code-square-icon">
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</template>

<template id="device-desktop-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-device-desktop">
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</template>

        <div class="position-relative">
                <ul
                  role="listbox"
                  class="ActionListWrap QueryBuilder-ListWrap"
                  aria-label="Suggestions"
                  data-action="
                    combobox-commit:query-builder#comboboxCommit
                    mousedown:query-builder#resultsMousedown
                  "
                  data-target="query-builder.resultsList"
                  data-persist-list=false
                  id="query-builder-test-results"
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          <div class="d-flex flex-row color-fg-muted px-3 text-small color-bg-default search-feedback-prompt">
            <a target="_blank" href="https://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax" data-view-component="true" class="Link color-fg-accent text-normal ml-2">Search syntax tips</a>            <div class="d-flex flex-1"></div>
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<dialog-helper>
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      <h1 class="Overlay-title " id="feedback-dialog-title">
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      <button data-close-dialog-id="feedback-dialog" aria-label="Close" type="button" data-view-component="true" class="close-button Overlay-closeButton"><svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x">
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      <scrollable-region data-labelled-by="feedback-dialog-title">
        <div data-view-component="true" class="Overlay-body">        <!-- '"` --><!-- </textarea></xmp> --></option></form><form id="code-search-feedback-form" data-turbo="false" action="/search/feedback" accept-charset="UTF-8" method="post"><input type="hidden" data-csrf="true" name="authenticity_token" value="PxJWgLik9hxdPBeh6f2sk/r6NncpMLlLGHL3Kp6TGl5UlyLAAY2Ut/oNPdZwd3MCn3SjombPDtcoHskUNHTGwg==" />
          <p>We read every piece of feedback, and take your input very seriously.</p>
          <textarea name="feedback" class="form-control width-full mb-2" style="height: 120px" id="feedback"></textarea>
          <input name="include_email" id="include_email" aria-label="Include my email address so I can be contacted" class="form-control mr-2" type="checkbox">
          <label for="include_email" style="font-weight: normal">Include my email address so I can be contacted</label>
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    <custom-scopes data-target="qbsearch-input.customScopesManager">
    
<dialog-helper>
  <dialog data-target="custom-scopes.customScopesModalDialog" data-action="close:qbsearch-input#handleDialogClose cancel:qbsearch-input#handleDialogClose" id="custom-scopes-dialog" aria-modal="true" aria-labelledby="custom-scopes-dialog-title" aria-describedby="custom-scopes-dialog-description" data-view-component="true" class="Overlay Overlay-whenNarrow Overlay--size-medium Overlay--motion-scaleFade Overlay--disableScroll">
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  <div class="Overlay-headerContentWrap">
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      <h1 class="Overlay-title " id="custom-scopes-dialog-title">
        Saved searches
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      <button data-close-dialog-id="custom-scopes-dialog" aria-label="Close" type="button" data-view-component="true" class="close-button Overlay-closeButton"><svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x">
    <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path>
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      <scrollable-region data-labelled-by="custom-scopes-dialog-title">
        <div data-view-component="true" class="Overlay-body">        <div data-target="custom-scopes.customScopesModalDialogFlash"></div>

        <div hidden class="create-custom-scope-form" data-target="custom-scopes.createCustomScopeForm">
        <!-- '"` --><!-- </textarea></xmp> --></option></form><form id="custom-scopes-dialog-form" data-turbo="false" action="/search/custom_scopes" accept-charset="UTF-8" method="post"><input type="hidden" data-csrf="true" name="authenticity_token" value="rNGrYngw46eGwNMJ+x8JoQ82lua21I8ClPmbhfLJX6A+3UdiDmjiMjMjjtABhG/L5yphKY5rOqDzjYgnkpSNsw==" />
          <div data-target="custom-scopes.customScopesModalDialogFlash"></div>

          <input type="hidden" id="custom_scope_id" name="custom_scope_id" data-target="custom-scopes.customScopesIdField">

          <div class="form-group">
            <label for="custom_scope_name">Name</label>
            <auto-check src="/search/custom_scopes/check_name" required>
              <input
                type="text"
                name="custom_scope_name"
                id="custom_scope_name"
                data-target="custom-scopes.customScopesNameField"
                class="form-control"
                autocomplete="off"
                placeholder="github-ruby"
                required
                maxlength="50">
              <input type="hidden" data-csrf="true" value="baLgkCIOgdSTU/WT2CMiniXvMud3/V9kV8hvpdDoR33f2346LlJ+HLLtcKn8aQ/jwosWxb0uEoaAmaSC4Y8oJA==" />
            </auto-check>
          </div>

          <div class="form-group">
            <label for="custom_scope_query">Query</label>
            <input
              type="text"
              name="custom_scope_query"
              id="custom_scope_query"
              data-target="custom-scopes.customScopesQueryField"
              class="form-control"
              autocomplete="off"
              placeholder="(repo:mona/a OR repo:mona/b) AND lang:python"
              required
              maxlength="500">
          </div>

          <p class="text-small color-fg-muted">
            To see all available qualifiers, see our <a class="Link--inTextBlock" href="https://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax">documentation</a>.
          </p>
</form>        </div>

        <div data-target="custom-scopes.manageCustomScopesForm">
          <div data-target="custom-scopes.list"></div>
        </div>

</div>
      </scrollable-region>
      <div data-view-component="true" class="Overlay-footer Overlay-footer--alignEnd Overlay-footer--divided">          <button data-action="click:custom-scopes#customScopesCancel" type="button" data-view-component="true" class="btn">    Cancel
</button>
          <button form="custom-scopes-dialog-form" data-action="click:custom-scopes#customScopesSubmit" data-target="custom-scopes.customScopesSubmitButton" type="submit" data-view-component="true" class="btn-primary btn">    Create saved search
</button>
</div>
</dialog></dialog-helper>
    </custom-scopes>
  </div>
</qbsearch-input>

            <div class="position-relative HeaderMenu-link-wrap d-lg-inline-block">
              <a
                href="/login?return_to=https%3A%2F%2Fgithub.com%2Finstanseg%2Finstanseg%2Fblob%2Fmain%2FREADME.md"
                class="HeaderMenu-link HeaderMenu-link--sign-in HeaderMenu-button flex-shrink-0 no-underline d-none d-lg-inline-flex border border-lg-0 rounded rounded-lg-0 px-2 py-1"
                style="margin-left: 12px;"
                data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header menu&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;originating_url&quot;:&quot;https://github.com/instanseg/instanseg/blob/main/README.md&quot;,&quot;user_id&quot;:null}}" data-hydro-click-hmac="708e7716e7fd3d4f8faaa1621a215a049a36287a498632ac7a35cb58be7acdbd"
                data-analytics-event="{&quot;category&quot;:&quot;Marketing nav&quot;,&quot;action&quot;:&quot;click to go to homepage&quot;,&quot;label&quot;:&quot;ref_page:Marketing;ref_cta:Sign in;ref_loc:Header&quot;}"
              >
                Sign in
              </a>
            </div>

              <a href="/signup?ref_cta=Sign+up&amp;ref_loc=header+logged+out&amp;ref_page=%2F%3Cuser-name%3E%2F%3Crepo-name%3E%2Fblob%2Fshow&amp;source=header-repo&amp;source_repo=instanseg%2Finstanseg"
                class="HeaderMenu-link HeaderMenu-link--sign-up HeaderMenu-button flex-shrink-0 d-flex d-lg-inline-flex no-underline border color-border-default rounded px-2 py-1"
                data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header menu&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;originating_url&quot;:&quot;https://github.com/instanseg/instanseg/blob/main/README.md&quot;,&quot;user_id&quot;:null}}" data-hydro-click-hmac="708e7716e7fd3d4f8faaa1621a215a049a36287a498632ac7a35cb58be7acdbd"
                data-analytics-event="{&quot;category&quot;:&quot;Sign up&quot;,&quot;action&quot;:&quot;click to sign up for account&quot;,&quot;label&quot;:&quot;ref_page:/&lt;user-name&gt;/&lt;repo-name&gt;/blob/show;ref_cta:Sign up;ref_loc:header logged out&quot;}"
              >
                Sign up
              </a>
          <button type="button" class="sr-only js-header-menu-focus-trap d-block d-lg-none">Reseting focus</button>
        </div>
      </div>
    </div>
  </div>
</header>

      <div hidden="hidden" data-view-component="true" class="js-stale-session-flash stale-session-flash flash flash-warn flash-full">
  
        <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-alert">
    <path d="M6.457 1.047c.659-1.234 2.427-1.234 3.086 0l6.082 11.378A1.75 1.75 0 0 1 14.082 15H1.918a1.75 1.75 0 0 1-1.543-2.575Zm1.763.707a.25.25 0 0 0-.44 0L1.698 13.132a.25.25 0 0 0 .22.368h12.164a.25.25 0 0 0 .22-.368Zm.53 3.996v2.5a.75.75 0 0 1-1.5 0v-2.5a.75.75 0 0 1 1.5 0ZM9 11a1 1 0 1 1-2 0 1 1 0 0 1 2 0Z"></path>
</svg>
        <span class="js-stale-session-flash-signed-in" hidden>You signed in with another tab or window. <a class="Link--inTextBlock" href="">Reload</a> to refresh your session.</span>
        <span class="js-stale-session-flash-signed-out" hidden>You signed out in another tab or window. <a class="Link--inTextBlock" href="">Reload</a> to refresh your session.</span>
        <span class="js-stale-session-flash-switched" hidden>You switched accounts on another tab or window. <a class="Link--inTextBlock" href="">Reload</a> to refresh your session.</span>

    <button id="icon-button-60ed68fc-fc92-4c13-8d62-60d6239a749a" aria-labelledby="tooltip-17962ce2-4a96-45dc-bf45-71f66c19ec68" type="button" data-view-component="true" class="Button Button--iconOnly Button--invisible Button--medium flash-close js-flash-close">  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x Button-visual">
    <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path>
</svg>
</button><tool-tip id="tooltip-17962ce2-4a96-45dc-bf45-71f66c19ec68" for="icon-button-60ed68fc-fc92-4c13-8d62-60d6239a749a" popover="manual" data-direction="s" data-type="label" data-view-component="true" class="sr-only position-absolute">Dismiss alert</tool-tip>


  
</div>
    </div>

  <div id="start-of-content" class="show-on-focus"></div>








    <div id="js-flash-container" class="flash-container" data-turbo-replace>


      <include-fragment  src="/settings/two_factor_authentication/holiday_warning_banner"></include-fragment>


  <template class="js-flash-template">
    
<div class="flash flash-full   {{ className }}">
  <div >
    <button autofocus class="flash-close js-flash-close" type="button" aria-label="Dismiss this message">
      <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x">
    <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path>
</svg>
    </button>
    <div aria-atomic="true" role="alert" class="js-flash-alert">
      
      <div>{{ message }}</div>

    </div>
  </div>
</div>
  </template>
</div>


    






  <div
    class="application-main "
    data-commit-hovercards-enabled
    data-discussion-hovercards-enabled
    data-issue-and-pr-hovercards-enabled
    data-project-hovercards-enabled
  >
        <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class="">
    <main id="js-repo-pjax-container" >
      
      
    

    






  
  <div id="repository-container-header"  class="pt-3 hide-full-screen" style="background-color: var(--page-header-bgColor, var(--color-page-header-bg));" data-turbo-replace>

      <div class="d-flex flex-nowrap flex-justify-end mb-3  px-3 px-lg-5" style="gap: 1rem;">

        <div class="flex-auto min-width-0 width-fit">
            
  <div class=" d-flex flex-wrap flex-items-center wb-break-word f3 text-normal">
      <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-repo color-fg-muted mr-2">
    <path d="M2 2.5A2.5 2.5 0 0 1 4.5 0h8.75a.75.75 0 0 1 .75.75v12.5a.75.75 0 0 1-.75.75h-2.5a.75.75 0 0 1 0-1.5h1.75v-2h-8a1 1 0 0 0-.714 1.7.75.75 0 1 1-1.072 1.05A2.495 2.495 0 0 1 2 11.5Zm10.5-1h-8a1 1 0 0 0-1 1v6.708A2.486 2.486 0 0 1 4.5 9h8ZM5 12.25a.25.25 0 0 1 .25-.25h3.5a.25.25 0 0 1 .25.25v3.25a.25.25 0 0 1-.4.2l-1.45-1.087a.249.249 0 0 0-.3 0L5.4 15.7a.25.25 0 0 1-.4-.2Z"></path>
</svg>
    
    <span class="author flex-self-stretch" itemprop="author">
      <a class="url fn" rel="author" data-hovercard-type="organization" data-hovercard-url="/orgs/instanseg/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/instanseg">
        instanseg
</a>    </span>
    <span class="mx-1 flex-self-stretch color-fg-muted">/</span>
    <strong itemprop="name" class="mr-2 flex-self-stretch">
      <a data-pjax="#repo-content-pjax-container" data-turbo-frame="repo-content-turbo-frame" href="/instanseg/instanseg">instanseg</a>
    </strong>

    <span></span><span class="Label Label--secondary v-align-middle mr-1">Public</span>
  </div>


        </div>

        <div id="repository-details-container" class="flex-shrink-0" data-turbo-replace style="max-width: 70%;">
            <ul class="pagehead-actions flex-shrink-0 d-none d-md-inline" style="padding: 2px 0;">
    
      

  <li>
            <a href="/login?return_to=%2Finstanseg%2Finstanseg" rel="nofollow" id="repository-details-watch-button" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;notification subscription menu watch&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;originating_url&quot;:&quot;https://github.com/instanseg/instanseg/blob/main/README.md&quot;,&quot;user_id&quot;:null}}" data-hydro-click-hmac="1a3d31cb9cca7e8edaf2050ada390b1756b5cb6679b58d5a0ea7f23c2470e920" aria-label="You must be signed in to change notification settings" data-view-component="true" class="btn-sm btn">    <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-bell mr-2">
    <path d="M8 16a2 2 0 0 0 1.985-1.75c.017-.137-.097-.25-.235-.25h-3.5c-.138 0-.252.113-.235.25A2 2 0 0 0 8 16ZM3 5a5 5 0 0 1 10 0v2.947c0 .05.015.098.042.139l1.703 2.555A1.519 1.519 0 0 1 13.482 13H2.518a1.516 1.516 0 0 1-1.263-2.36l1.703-2.554A.255.255 0 0 0 3 7.947Zm5-3.5A3.5 3.5 0 0 0 4.5 5v2.947c0 .346-.102.683-.294.97l-1.703 2.556a.017.017 0 0 0-.003.01l.001.006c0 .002.002.004.004.006l.006.004.007.001h10.964l.007-.001.006-.004.004-.006.001-.007a.017.017 0 0 0-.003-.01l-1.703-2.554a1.745 1.745 0 0 1-.294-.97V5A3.5 3.5 0 0 0 8 1.5Z"></path>
</svg>Notifications
</a>    <tool-tip id="tooltip-36ee8652-986c-4919-8474-04647533f3e8" for="repository-details-watch-button" popover="manual" data-direction="s" data-type="description" data-view-component="true" class="sr-only position-absolute">You must be signed in to change notification settings</tool-tip>

  </li>

  <li>
          <a icon="repo-forked" id="fork-button" href="/login?return_to=%2Finstanseg%2Finstanseg" rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;repo details fork button&quot;,&quot;repository_id&quot;:846078299,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;originating_url&quot;:&quot;https://github.com/instanseg/instanseg/blob/main/README.md&quot;,&quot;user_id&quot;:null}}" data-hydro-click-hmac="bb5fed979486e0782b0cb07ee73052fe18ce6b46ba1455032c4a0165b9498a95" data-view-component="true" class="btn-sm btn">    <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-repo-forked mr-2">
    <path d="M5 5.372v.878c0 .414.336.75.75.75h4.5a.75.75 0 0 0 .75-.75v-.878a2.25 2.25 0 1 1 1.5 0v.878a2.25 2.25 0 0 1-2.25 2.25h-1.5v2.128a2.251 2.251 0 1 1-1.5 0V8.5h-1.5A2.25 2.25 0 0 1 3.5 6.25v-.878a2.25 2.25 0 1 1 1.5 0ZM5 3.25a.75.75 0 1 0-1.5 0 .75.75 0 0 0 1.5 0Zm6.75.75a.75.75 0 1 0 0-1.5.75.75 0 0 0 0 1.5Zm-3 8.75a.75.75 0 1 0-1.5 0 .75.75 0 0 0 1.5 0Z"></path>
</svg>Fork
    <span id="repo-network-counter" data-pjax-replace="true" data-turbo-replace="true" title="18" data-view-component="true" class="Counter">18</span>
</a>
  </li>

  <li>
        <div data-view-component="true" class="BtnGroup d-flex">
        <a href="/login?return_to=%2Finstanseg%2Finstanseg" rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;star button&quot;,&quot;repository_id&quot;:846078299,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;originating_url&quot;:&quot;https://github.com/instanseg/instanseg/blob/main/README.md&quot;,&quot;user_id&quot;:null}}" data-hydro-click-hmac="65b11b44708f6cf2db9e8642f8df77b48304a5cdf953b20ab6b2881c3cb46427" aria-label="You must be signed in to star a repository" data-view-component="true" class="tooltipped tooltipped-sw btn-sm btn">    <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-star v-align-text-bottom d-inline-block mr-2">
    <path d="M8 .25a.75.75 0 0 1 .673.418l1.882 3.815 4.21.612a.75.75 0 0 1 .416 1.279l-3.046 2.97.719 4.192a.751.751 0 0 1-1.088.791L8 12.347l-3.766 1.98a.75.75 0 0 1-1.088-.79l.72-4.194L.818 6.374a.75.75 0 0 1 .416-1.28l4.21-.611L7.327.668A.75.75 0 0 1 8 .25Zm0 2.445L6.615 5.5a.75.75 0 0 1-.564.41l-3.097.45 2.24 2.184a.75.75 0 0 1 .216.664l-.528 3.084 2.769-1.456a.75.75 0 0 1 .698 0l2.77 1.456-.53-3.084a.75.75 0 0 1 .216-.664l2.24-2.183-3.096-.45a.75.75 0 0 1-.564-.41L8 2.694Z"></path>
</svg><span data-view-component="true" class="d-inline">
          Star
</span>          <span id="repo-stars-counter-star" aria-label="124 users starred this repository" data-singular-suffix="user starred this repository" data-plural-suffix="users starred this repository" data-turbo-replace="true" title="124" data-view-component="true" class="Counter js-social-count">124</span>
</a></div>
  </li>

</ul>

        </div>
      </div>

        <div id="responsive-meta-container" data-turbo-replace>
</div>


          <nav data-pjax="#js-repo-pjax-container" aria-label="Repository" data-view-component="true" class="js-repo-nav js-sidenav-container-pjax js-responsive-underlinenav overflow-hidden UnderlineNav px-3 px-md-4 px-lg-5">

  <ul data-view-component="true" class="UnderlineNav-body list-style-none">
      <li data-view-component="true" class="d-inline-flex">
  <a id="code-tab" href="/instanseg/instanseg" data-tab-item="i0code-tab" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches repo_packages repo_deployments repo_attestations /instanseg/instanseg" data-pjax="#repo-content-pjax-container" data-turbo-frame="repo-content-turbo-frame" data-hotkey="g c" data-analytics-event="{&quot;category&quot;:&quot;Underline navbar&quot;,&quot;action&quot;:&quot;Click tab&quot;,&quot;label&quot;:&quot;Code&quot;,&quot;target&quot;:&quot;UNDERLINE_NAV.TAB&quot;}" aria-current="page" data-view-component="true" class="UnderlineNav-item no-wrap js-responsive-underlinenav-item js-selected-navigation-item selected">
    
              <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-code UnderlineNav-octicon d-none d-sm-inline">
    <path d="m11.28 3.22 4.25 4.25a.75.75 0 0 1 0 1.06l-4.25 4.25a.749.749 0 0 1-1.275-.326.749.749 0 0 1 .215-.734L13.94 8l-3.72-3.72a.749.749 0 0 1 .326-1.275.749.749 0 0 1 .734.215Zm-6.56 0a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042L2.06 8l3.72 3.72a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L.47 8.53a.75.75 0 0 1 0-1.06Z"></path>
</svg>
        <span data-content="Code">Code</span>
          <span id="code-repo-tab-count" data-pjax-replace="" data-turbo-replace="" title="Not available" data-view-component="true" class="Counter"></span>


    
</a></li>
      <li data-view-component="true" class="d-inline-flex">
  <a id="issues-tab" href="/instanseg/instanseg/issues" data-tab-item="i1issues-tab" data-selected-links="repo_issues repo_labels repo_milestones /instanseg/instanseg/issues" data-pjax="#repo-content-pjax-container" data-turbo-frame="repo-content-turbo-frame" data-hotkey="g i" data-analytics-event="{&quot;category&quot;:&quot;Underline navbar&quot;,&quot;action&quot;:&quot;Click tab&quot;,&quot;label&quot;:&quot;Issues&quot;,&quot;target&quot;:&quot;UNDERLINE_NAV.TAB&quot;}" data-view-component="true" class="UnderlineNav-item no-wrap js-responsive-underlinenav-item js-selected-navigation-item">
    
              <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-issue-opened UnderlineNav-octicon d-none d-sm-inline">
    <path d="M8 9.5a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Z"></path><path d="M8 0a8 8 0 1 1 0 16A8 8 0 0 1 8 0ZM1.5 8a6.5 6.5 0 1 0 13 0 6.5 6.5 0 0 0-13 0Z"></path>
</svg>
        <span data-content="Issues">Issues</span>
          <span id="issues-repo-tab-count" data-pjax-replace="" data-turbo-replace="" title="7" data-view-component="true" class="Counter">7</span>


    
</a></li>
      <li data-view-component="true" class="d-inline-flex">
  <a id="pull-requests-tab" href="/instanseg/instanseg/pulls" data-tab-item="i2pull-requests-tab" data-selected-links="repo_pulls checks /instanseg/instanseg/pulls" data-pjax="#repo-content-pjax-container" data-turbo-frame="repo-content-turbo-frame" data-hotkey="g p" data-analytics-event="{&quot;category&quot;:&quot;Underline navbar&quot;,&quot;action&quot;:&quot;Click tab&quot;,&quot;label&quot;:&quot;Pull requests&quot;,&quot;target&quot;:&quot;UNDERLINE_NAV.TAB&quot;}" data-view-component="true" class="UnderlineNav-item no-wrap js-responsive-underlinenav-item js-selected-navigation-item">
    
              <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-git-pull-request UnderlineNav-octicon d-none d-sm-inline">
    <path d="M1.5 3.25a2.25 2.25 0 1 1 3 2.122v5.256a2.251 2.251 0 1 1-1.5 0V5.372A2.25 2.25 0 0 1 1.5 3.25Zm5.677-.177L9.573.677A.25.25 0 0 1 10 .854V2.5h1A2.5 2.5 0 0 1 13.5 5v5.628a2.251 2.251 0 1 1-1.5 0V5a1 1 0 0 0-1-1h-1v1.646a.25.25 0 0 1-.427.177L7.177 3.427a.25.25 0 0 1 0-.354ZM3.75 2.5a.75.75 0 1 0 0 1.5.75.75 0 0 0 0-1.5Zm0 9.5a.75.75 0 1 0 0 1.5.75.75 0 0 0 0-1.5Zm8.25.75a.75.75 0 1 0 1.5 0 .75.75 0 0 0-1.5 0Z"></path>
</svg>
        <span data-content="Pull requests">Pull requests</span>
          <span id="pull-requests-repo-tab-count" data-pjax-replace="" data-turbo-replace="" title="5" data-view-component="true" class="Counter">5</span>


    
</a></li>
      <li data-view-component="true" class="d-inline-flex">
  <a id="actions-tab" href="/instanseg/instanseg/actions" data-tab-item="i3actions-tab" data-selected-links="repo_actions /instanseg/instanseg/actions" data-pjax="#repo-content-pjax-container" data-turbo-frame="repo-content-turbo-frame" data-hotkey="g a" data-analytics-event="{&quot;category&quot;:&quot;Underline navbar&quot;,&quot;action&quot;:&quot;Click tab&quot;,&quot;label&quot;:&quot;Actions&quot;,&quot;target&quot;:&quot;UNDERLINE_NAV.TAB&quot;}" data-view-component="true" class="UnderlineNav-item no-wrap js-responsive-underlinenav-item js-selected-navigation-item">
    
              <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-play UnderlineNav-octicon d-none d-sm-inline">
    <path d="M8 0a8 8 0 1 1 0 16A8 8 0 0 1 8 0ZM1.5 8a6.5 6.5 0 1 0 13 0 6.5 6.5 0 0 0-13 0Zm4.879-2.773 4.264 2.559a.25.25 0 0 1 0 .428l-4.264 2.559A.25.25 0 0 1 6 10.559V5.442a.25.25 0 0 1 .379-.215Z"></path>
</svg>
        <span data-content="Actions">Actions</span>
          <span id="actions-repo-tab-count" data-pjax-replace="" data-turbo-replace="" title="Not available" data-view-component="true" class="Counter"></span>


    
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target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://github.com/ThibautGoldsborough/instanseg_thibaut/blob/main/assets/instanseg_logo.png?raw=True\"\u003e\u003cimg src=\"https://github.com/ThibautGoldsborough/instanseg_thibaut/raw/main/assets/instanseg_logo.png?raw=True\" alt=\"Instanseg Logo\" width=\"25%\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eOverview\u003c/h2\u003e\u003ca id=\"user-content-overview\" class=\"anchor\" aria-label=\"Permalink: Overview\" href=\"#overview\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eInstanSeg is a pytorch-based cell and nucleus segmentation pipeline for fluorescence and brightfield microscopy images. This README provides instructions for setting up the environment, installing dependencies, and using the provided tools and models.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eWhy should I use InstanSeg?\u003c/h2\u003e\u003ca id=\"user-content-why-should-i-use-instanseg\" class=\"anchor\" aria-label=\"Permalink: Why should I use InstanSeg?\" href=\"#why-should-i-use-instanseg\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003col dir=\"auto\"\u003e\n\u003cli\u003eInstanSeg is freely available and open source.\u003c/li\u003e\n\u003cli\u003eIt's faster than other cell segmentation methods… sometimes much faster.\u003c/li\u003e\n\u003cli\u003eIt's capable of accurately segmenting both nuclei and whole cells.\u003c/li\u003e\n\u003cli\u003eInstanSeg can be entirely compiled in TorchScript - including postprocessing! This means it's not only easy to use in Python but also works with LibTorch alone. This allows you to run InstanSeg directly in QuPath!\u003c/li\u003e\n\u003cli\u003eYou can use InstanSeg on multiplexed images (images that have more than three channels) on novel biomarker panels, without retraining or manual intervention.\u003c/li\u003e\n\u003cli\u003eWe plan to release more InstanSeg models trained on public datasets. If there's a nucleus and/or cell segmentation dataset under a permissive open license (e.g. CC0 or CC-BY) that we missed, let us know, and we may be able to increase our InstanSeg model zoo.\u003c/li\u003e\n\u003c/ol\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eInstanSeg has its own QuPath extension!\u003c/h2\u003e\u003ca id=\"user-content-instanseg-has-its-own-qupath-extension\" class=\"anchor\" aria-label=\"Permalink: InstanSeg has its own QuPath extension!\" href=\"#instanseg-has-its-own-qupath-extension\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eInstanSeg is introduced in the \u003ca href=\"https://github.com/qupath/qupath/releases/tag/v0.6.0-rc2\"\u003eQuPath pre-release v0.6.0-rc2\u003c/a\u003e, so you can start using InstanSeg immediately. You can find the QuPath extension source code \u003ca href=\"https://github.com/qupath/qupath-extension-instanseg\"\u003ein its GitHub repository\u003c/a\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eHow to cite InstanSeg:\u003c/h2\u003e\u003ca id=\"user-content-how-to-cite-instanseg\" class=\"anchor\" aria-label=\"Permalink: How to cite InstanSeg:\" href=\"#how-to-cite-instanseg\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eIf you use InstanSeg for nucleus segmentation of brightfield histology images, please cite:\u003c/p\u003e\n\u003cblockquote\u003e\n\u003cp dir=\"auto\"\u003eGoldsborough, T. et al. (2024) ‘InstanSeg: an embedding-based instance segmentation algorithm optimized for accurate, efficient and portable cell segmentation’. \u003cem\u003earXiv\u003c/em\u003e. Available at: \u003ca href=\"https://doi.org/10.48550/arXiv.2408.15954\" rel=\"nofollow\"\u003ehttps://doi.org/10.48550/arXiv.2408.15954\u003c/a\u003e.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003cp dir=\"auto\"\u003eIf you use InstanSeg for nucleus and/or cell segmentation in fluorescence images, please cite:\u003c/p\u003e\n\u003cblockquote\u003e\n\u003cp dir=\"auto\"\u003eGoldsborough, T. et al. (2024) ‘A novel channel invariant architecture for the segmentation of cells and nuclei in multiplexed images using InstanSeg’. \u003cem\u003ebioRxiv\u003c/em\u003e, p. 2024.09.04.611150. Available at: \u003ca href=\"https://doi.org/10.1101/2024.09.04.611150\" rel=\"nofollow\"\u003ehttps://doi.org/10.1101/2024.09.04.611150\u003c/a\u003e.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003cp align=\"center\" dir=\"auto\"\u003e\n  \u003ca target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://github.com/ThibautGoldsborough/instanseg_thibaut/blob/main/assets/instanseg_main_figure.png?raw=True\"\u003e\u003cimg src=\"https://github.com/ThibautGoldsborough/instanseg_thibaut/raw/main/assets/instanseg_main_figure.png?raw=True\" alt=\"Instanseg Main Figure\" width=\"50%\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eTable of Contents\u003c/h2\u003e\u003ca id=\"user-content-table-of-contents\" class=\"anchor\" aria-label=\"Permalink: Table of Contents\" href=\"#table-of-contents\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#overview\"\u003eOverview\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#why-should-i-use-instanseg\"\u003eWhy should I use InstanSeg?\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#instanseg-has-its-own-qupath-extension\"\u003eInstanSeg has its own QuPath extension!\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#how-to-cite-instanseg\"\u003eHow to cite InstanSeg:\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#table-of-contents\"\u003eTable of Contents\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#installing-using-pip\"\u003eInstalling using pip\u003c/a\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#local-installation\"\u003eLocal Installation\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#gpu-version-cuda-for-windows-and-linux\"\u003eGPU Version (CUDA) for Windows and Linux\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#setup-repository\"\u003eSetup Repository\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#usage\"\u003eUsage\u003c/a\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#download-datasets\"\u003eDownload Datasets\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#training-models\"\u003eTraining Models\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#testing-models\"\u003eTesting Models\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#using-instanseg-for-inference\"\u003eUsing InstanSeg for inference\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#model-versioning\"\u003eModel versioning\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eInstalling using pip\u003c/h2\u003e\u003ca id=\"user-content-installing-using-pip\" class=\"anchor\" aria-label=\"Permalink: Installing using pip\" href=\"#installing-using-pip\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eFor a minimal installation:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"pip install instanseg-torch\"\u003e\u003cpre\u003epip install instanseg-torch\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eif you want all the requirements used for training:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"pip install instanseg-torch[full]\"\u003e\u003cpre\u003epip install instanseg-torch[full]\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eYou can get started immediately by calling the InstanSeg class:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-python notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"from instanseg import InstanSeg\ninstanseg_brightfield = InstanSeg(\u0026quot;brightfield_nuclei\u0026quot;, image_reader= \u0026quot;tiffslide\u0026quot;, verbosity=1)\n\nlabeled_output = instanseg_brightfield.eval(image = \u0026quot;../instanseg/examples/HE_example.tif\u0026quot;,\n                                            save_output = True,\n                                            save_overlay = True)\"\u003e\u003cpre\u003e\u003cspan class=\"pl-k\"\u003efrom\u003c/span\u003e \u003cspan class=\"pl-s1\"\u003einstanseg\u003c/span\u003e \u003cspan class=\"pl-k\"\u003eimport\u003c/span\u003e \u003cspan class=\"pl-v\"\u003eInstanSeg\u003c/span\u003e\n\u003cspan class=\"pl-s1\"\u003einstanseg_brightfield\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e \u003cspan class=\"pl-en\"\u003eInstanSeg\u003c/span\u003e(\u003cspan class=\"pl-s\"\u003e\"brightfield_nuclei\"\u003c/span\u003e, \u003cspan class=\"pl-s1\"\u003eimage_reader\u003c/span\u003e\u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e \u003cspan class=\"pl-s\"\u003e\"tiffslide\"\u003c/span\u003e, \u003cspan class=\"pl-s1\"\u003everbosity\u003c/span\u003e\u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e\u003cspan class=\"pl-c1\"\u003e1\u003c/span\u003e)\n\n\u003cspan class=\"pl-s1\"\u003elabeled_output\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e \u003cspan class=\"pl-s1\"\u003einstanseg_brightfield\u003c/span\u003e.\u003cspan class=\"pl-c1\"\u003eeval\u003c/span\u003e(\u003cspan class=\"pl-s1\"\u003eimage\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e \u003cspan class=\"pl-s\"\u003e\"../instanseg/examples/HE_example.tif\"\u003c/span\u003e,\n                                            \u003cspan class=\"pl-s1\"\u003esave_output\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003eTrue\u003c/span\u003e,\n                                            \u003cspan class=\"pl-s1\"\u003esave_overlay\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003eTrue\u003c/span\u003e)\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eAlternatively, if you want more control over the intermediate steps:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-python notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"image_array, pixel_size = instanseg_brightfield.read_image(\u0026quot;../instanseg/examples/HE_example.tif\u0026quot;)\n\nlabeled_output, image_tensor  = instanseg_brightfield.eval_small_image(image_array, pixel_size)\n\ndisplay = instanseg_brightfield.display(image_tensor, labeled_output)\n\nfrom instanseg.utils.utils import show_images\nshow_images(image_tensor,display, colorbar=False, titles = [\u0026quot;Normalized Image\u0026quot;, \u0026quot;Image with segmentation\u0026quot;])\"\u003e\u003cpre\u003e\u003cspan class=\"pl-s1\"\u003eimage_array\u003c/span\u003e, \u003cspan class=\"pl-s1\"\u003epixel_size\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e \u003cspan class=\"pl-s1\"\u003einstanseg_brightfield\u003c/span\u003e.\u003cspan class=\"pl-c1\"\u003eread_image\u003c/span\u003e(\u003cspan class=\"pl-s\"\u003e\"../instanseg/examples/HE_example.tif\"\u003c/span\u003e)\n\n\u003cspan class=\"pl-s1\"\u003elabeled_output\u003c/span\u003e, \u003cspan class=\"pl-s1\"\u003eimage_tensor\u003c/span\u003e  \u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e \u003cspan class=\"pl-s1\"\u003einstanseg_brightfield\u003c/span\u003e.\u003cspan class=\"pl-c1\"\u003eeval_small_image\u003c/span\u003e(\u003cspan class=\"pl-s1\"\u003eimage_array\u003c/span\u003e, \u003cspan class=\"pl-s1\"\u003epixel_size\u003c/span\u003e)\n\n\u003cspan class=\"pl-s1\"\u003edisplay\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e \u003cspan class=\"pl-s1\"\u003einstanseg_brightfield\u003c/span\u003e.\u003cspan class=\"pl-c1\"\u003edisplay\u003c/span\u003e(\u003cspan class=\"pl-s1\"\u003eimage_tensor\u003c/span\u003e, \u003cspan class=\"pl-s1\"\u003elabeled_output\u003c/span\u003e)\n\n\u003cspan class=\"pl-k\"\u003efrom\u003c/span\u003e \u003cspan class=\"pl-s1\"\u003einstanseg\u003c/span\u003e.\u003cspan class=\"pl-s1\"\u003eutils\u003c/span\u003e.\u003cspan class=\"pl-s1\"\u003eutils\u003c/span\u003e \u003cspan class=\"pl-k\"\u003eimport\u003c/span\u003e \u003cspan class=\"pl-s1\"\u003eshow_images\u003c/span\u003e\n\u003cspan class=\"pl-en\"\u003eshow_images\u003c/span\u003e(\u003cspan class=\"pl-s1\"\u003eimage_tensor\u003c/span\u003e,\u003cspan class=\"pl-s1\"\u003edisplay\u003c/span\u003e, \u003cspan class=\"pl-s1\"\u003ecolorbar\u003c/span\u003e\u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e\u003cspan class=\"pl-c1\"\u003eFalse\u003c/span\u003e, \u003cspan class=\"pl-s1\"\u003etitles\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e=\u003c/span\u003e [\u003cspan class=\"pl-s\"\u003e\"Normalized Image\"\u003c/span\u003e, \u003cspan class=\"pl-s\"\u003e\"Image with segmentation\"\u003c/span\u003e])\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eLocal Installation\u003c/h3\u003e\u003ca id=\"user-content-local-installation\" class=\"anchor\" aria-label=\"Permalink: Local Installation\" href=\"#local-installation\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo install InstanSeg locally, follow these steps:\u003c/p\u003e\n\u003col dir=\"auto\"\u003e\n\u003cli\u003e\n\u003cp dir=\"auto\"\u003eInstall either Anaconda, Mamba, or \u003ca href=\"https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html\" rel=\"nofollow\"\u003emicromamba\u003c/a\u003e. We use micromamba for speed and simplicity, but you can replace \"micromamba\" with the distribution you are using.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp dir=\"auto\"\u003eIn your terminal or Anaconda prompt on Windows, create a new environment and install dependencies using the provided \u003ccode\u003eenv.yml\u003c/code\u003e file:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"micromamba create -n instanseg --file env.yml\"\u003e\u003cpre\u003emicromamba create -n instanseg --file env.yml\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp dir=\"auto\"\u003eActivate your environment:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"micromamba activate instanseg\"\u003e\u003cpre\u003emicromamba activate instanseg\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eGPU Version (CUDA) for Windows and Linux\u003c/h3\u003e\u003ca id=\"user-content-gpu-version-cuda-for-windows-and-linux\" class=\"anchor\" aria-label=\"Permalink: GPU Version (CUDA) for Windows and Linux\" href=\"#gpu-version-cuda-for-windows-and-linux\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eIf you intend to use GPU acceleration and CUDA, follow these additional steps:\u003c/p\u003e\n\u003col start=\"4\" dir=\"auto\"\u003e\n\u003cli\u003e\n\u003cp dir=\"auto\"\u003eUninstall existing PyTorch and reinstall with CUDA support:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"micromamba remove pytorch torchvision monai\nmicromamba install pytorch==2.1.1 torchvision==0.16.1 monai=1.3.0 pytorch-cuda=12.1 -c conda-forge -c pytorch -c nvidia\npip install cupy-cuda12x\"\u003e\u003cpre\u003emicromamba remove pytorch torchvision monai\nmicromamba install pytorch==2.1.1 torchvision==0.16.1 monai=1.3.0 pytorch-cuda=12.1 -c conda-forge -c pytorch -c nvidia\npip install cupy-cuda12x\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp dir=\"auto\"\u003eCheck if CUDA is available:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"python -c \u0026quot;import torch; print('CUDA is available') if torch.cuda.is_available() else print('CUDA is not available')\u0026quot;\"\u003e\u003cpre\u003epython -c \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eimport torch; print('CUDA is available') if torch.cuda.is_available() else print('CUDA is not available')\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp dir=\"auto\"\u003eThe repository may work with older versions of CUDA. For this replace \"12.1\" and \"12\" with the required version.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eSetup Repository\u003c/h3\u003e\u003ca id=\"user-content-setup-repository\" class=\"anchor\" aria-label=\"Permalink: Setup Repository\" href=\"#setup-repository\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003col start=\"3\" dir=\"auto\"\u003e\n\u003cli\u003eBuild repository:\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"pip install -e .\"\u003e\u003cpre\u003epip install -e \u003cspan class=\"pl-c1\"\u003e.\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eUsage\u003c/h2\u003e\u003ca id=\"user-content-usage\" class=\"anchor\" aria-label=\"Permalink: Usage\" href=\"#usage\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eDownload Datasets\u003c/h3\u003e\u003ca id=\"user-content-download-datasets\" class=\"anchor\" aria-label=\"Permalink: Download Datasets\" href=\"#download-datasets\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo download public datasets and example images, follow the instructions under \u003cstrong\u003einstanseg/notebooks/load_datasets.ipynb\u003c/strong\u003e\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eTo train InstanSeg on your own dataset, extend the \u003cstrong\u003einstanseg/notebooks/load_datasets.ipynb\u003c/strong\u003e with one of the templates provided.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eTraining Models\u003c/h3\u003e\u003ca id=\"user-content-training-models\" class=\"anchor\" aria-label=\"Permalink: Training Models\" href=\"#training-models\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo train models using InstanSeg, use the \u003cstrong\u003etrain.py\u003c/strong\u003e script under the scripts folder.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eFor example, to train InstanSeg on the TNBC_2018 dataset over 250 epochs at a pixel resolution of 0.25 microns/pixel, run the following command:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"cd instanseg/scripts\npython train.py -data segmentation_dataset.pth -source \u0026quot;[TNBC_2018]\u0026quot; --num_epochs 250 --experiment_str my_first_instanseg --requested_pixel_size 0.25\"\u003e\u003cpre\u003e\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e instanseg/scripts\npython train.py -data segmentation_dataset.pth -source \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e[TNBC_2018]\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e --num_epochs 250 --experiment_str my_first_instanseg --requested_pixel_size 0.25\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo train a channel invariant InstanSeg on the CPDMI_2023 dataset, predicting both nuclei and cells, run the following command:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"cd instanseg/scripts\npython train.py -data segmentation_dataset.pth -source \u0026quot;[CPDMI_2023]\u0026quot; --num_epochs 250 --experiment_str my_first_instanseg -target NC --channel_invariant True --requested_pixel_size 0.5\"\u003e\u003cpre\u003e\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e instanseg/scripts\npython train.py -data segmentation_dataset.pth -source \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e[CPDMI_2023]\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e --num_epochs 250 --experiment_str my_first_instanseg -target NC --channel_invariant True --requested_pixel_size 0.5\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eEach epoch should take approximately 1 to 3 minutes to complete (with mps or cuda support).\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eFor more options and configurations, refer to the parser arguments in the train.py file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eTesting Models\u003c/h3\u003e\u003ca id=\"user-content-testing-models\" class=\"anchor\" aria-label=\"Permalink: Testing Models\" href=\"#testing-models\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo test trained models and obtain F1 metrics, use the following command:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"python test.py --model_folder my_first_instanseg -test_set Validation --optimize_hyperparameters True\npython test.py --model_folder my_first_instanseg -test_set Test --params best_params\"\u003e\u003cpre\u003epython test.py --model_folder my_first_instanseg -test_set Validation --optimize_hyperparameters True\npython test.py --model_folder my_first_instanseg -test_set Test --params best_params\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eUsing InstanSeg for inference\u003c/h3\u003e\u003ca id=\"user-content-using-instanseg-for-inference\" class=\"anchor\" aria-label=\"Permalink: Using InstanSeg for inference\" href=\"#using-instanseg-for-inference\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"python inference.py --model_folder my_first_instanseg --image_path ../examples\"\u003e\u003cpre\u003epython inference.py --model_folder my_first_instanseg --image_path ../examples\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eReplace \"../examples\" with the path to your images. If InstanSeg cannot read the image pixel size from the image metadata, the user is required to provide a --pixel_size parameter. InstanSeg provides (limited) support for whole slide images (WSIs). For more options and configurations, refer to the parser arguments in the inference.py file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eModel versioning\u003c/h3\u003e\u003ca id=\"user-content-model-versioning\" class=\"anchor\" aria-label=\"Permalink: Model versioning\" href=\"#model-versioning\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eLinks to different model versions are stored in \u003ccode\u003einstanseg/models/model-index.json\u003c/code\u003e. When releasing new models,\nyou should add entries to this JSON file, optionally removing any previous versions that shouldn't be available in future versions.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eAn example entry looks like this:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-json notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"{\n  \u0026quot;name\u0026quot;: \u0026quot;[MODEL_NAME]\u0026quot;,\n  \u0026quot;url\u0026quot;: \u0026quot;https://github.com/instanseg/instanseg/releases/download/[RELEASE_NAME]/[MODEL_NAME].zip\u0026quot;,\n  \u0026quot;version\u0026quot;: \u0026quot;0.1.0\u0026quot;,\n  \u0026quot;license\u0026quot;: \u0026quot;Apache-2.0\u0026quot;\n}\"\u003e\u003cpre\u003e{\n  \u003cspan class=\"pl-ent\"\u003e\"name\"\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e[MODEL_NAME]\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n  \u003cspan class=\"pl-ent\"\u003e\"url\"\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003ehttps://github.com/instanseg/instanseg/releases/download/[RELEASE_NAME]/[MODEL_NAME].zip\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n  \u003cspan class=\"pl-ent\"\u003e\"version\"\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e0.1.0\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n  \u003cspan class=\"pl-ent\"\u003e\"license\"\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eApache-2.0\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n}\u003c/pre\u003e\u003c/div\u003e\n\u003c/article\u003e","renderedFileInfo":null,"shortPath":null,"symbolsEnabled":true,"tabSize":8,"topBannersInfo":{"overridingGlobalFundingFile":false,"globalPreferredFundingPath":null,"showInvalidCitationWarning":false,"citationHelpUrl":"https://docs.github.com/github/creating-cloning-and-archiving-repositories/creating-a-repository-on-github/about-citation-files","actionsOnboardingTip":null},"truncated":false,"viewable":true,"workflowRedirectUrl":null,"symbols":{"timed_out":false,"not_analyzed":false,"symbols":[{"name":"Overview","kind":"section_2","ident_start":180,"ident_end":188,"extent_start":177,"extent_end":443,"fully_qualified_name":"Overview","ident_utf16":{"start":{"line_number":7,"utf16_col":3},"end":{"line_number":7,"utf16_col":11}},"extent_utf16":{"start":{"line_number":7,"utf16_col":0},"end":{"line_number":11,"utf16_col":0}}},{"name":"Why should I use 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</p>
<div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Overview</h2><a id="user-content-overview" class="anchor" aria-label="Permalink: Overview" href="#overview"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<p dir="auto">InstanSeg is a pytorch-based cell and nucleus segmentation pipeline for fluorescence and brightfield microscopy images. This README provides instructions for setting up the environment, installing dependencies, and using the provided tools and models.</p>
<div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Why should I use InstanSeg?</h2><a id="user-content-why-should-i-use-instanseg" class="anchor" aria-label="Permalink: Why should I use InstanSeg?" href="#why-should-i-use-instanseg"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<ol dir="auto">
<li>InstanSeg is freely available and open source.</li>
<li>It's faster than other cell segmentation methods… sometimes much faster.</li>
<li>It's capable of accurately segmenting both nuclei and whole cells.</li>
<li>InstanSeg can be entirely compiled in TorchScript - including postprocessing! This means it's not only easy to use in Python but also works with LibTorch alone. This allows you to run InstanSeg directly in QuPath!</li>
<li>You can use InstanSeg on multiplexed images (images that have more than three channels) on novel biomarker panels, without retraining or manual intervention.</li>
<li>We plan to release more InstanSeg models trained on public datasets. If there's a nucleus and/or cell segmentation dataset under a permissive open license (e.g. CC0 or CC-BY) that we missed, let us know, and we may be able to increase our InstanSeg model zoo.</li>
</ol>
<div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">InstanSeg has its own QuPath extension!</h2><a id="user-content-instanseg-has-its-own-qupath-extension" class="anchor" aria-label="Permalink: InstanSeg has its own QuPath extension!" href="#instanseg-has-its-own-qupath-extension"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<p dir="auto">InstanSeg is introduced in the <a href="https://github.com/qupath/qupath/releases/tag/v0.6.0-rc2">QuPath pre-release v0.6.0-rc2</a>, so you can start using InstanSeg immediately. You can find the QuPath extension source code <a href="https://github.com/qupath/qupath-extension-instanseg">in its GitHub repository</a>.</p>
<div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">How to cite InstanSeg:</h2><a id="user-content-how-to-cite-instanseg" class="anchor" aria-label="Permalink: How to cite InstanSeg:" href="#how-to-cite-instanseg"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<p dir="auto">If you use InstanSeg for nucleus segmentation of brightfield histology images, please cite:</p>
<blockquote>
<p dir="auto">Goldsborough, T. et al. (2024) ‘InstanSeg: an embedding-based instance segmentation algorithm optimized for accurate, efficient and portable cell segmentation’. <em>arXiv</em>. Available at: <a href="https://doi.org/10.48550/arXiv.2408.15954" rel="nofollow">https://doi.org/10.48550/arXiv.2408.15954</a>.</p>
</blockquote>
<p dir="auto">If you use InstanSeg for nucleus and/or cell segmentation in fluorescence images, please cite:</p>
<blockquote>
<p dir="auto">Goldsborough, T. et al. (2024) ‘A novel channel invariant architecture for the segmentation of cells and nuclei in multiplexed images using InstanSeg’. <em>bioRxiv</em>, p. 2024.09.04.611150. Available at: <a href="https://doi.org/10.1101/2024.09.04.611150" rel="nofollow">https://doi.org/10.1101/2024.09.04.611150</a>.</p>
</blockquote>
<p align="center" dir="auto">
  <a target="_blank" rel="noopener noreferrer" href="https://github.com/ThibautGoldsborough/instanseg_thibaut/blob/main/assets/instanseg_main_figure.png?raw=True"><img src="https://github.com/ThibautGoldsborough/instanseg_thibaut/raw/main/assets/instanseg_main_figure.png?raw=True" alt="Instanseg Main Figure" width="50%" style="max-width: 100%;"></a>
</p>
<div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Table of Contents</h2><a id="user-content-table-of-contents" class="anchor" aria-label="Permalink: Table of Contents" href="#table-of-contents"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<ul dir="auto">
<li><a href="#overview">Overview</a></li>
<li><a href="#why-should-i-use-instanseg">Why should I use InstanSeg?</a></li>
<li><a href="#instanseg-has-its-own-qupath-extension">InstanSeg has its own QuPath extension!</a></li>
<li><a href="#how-to-cite-instanseg">How to cite InstanSeg:</a></li>
<li><a href="#table-of-contents">Table of Contents</a></li>
<li><a href="#installing-using-pip">Installing using pip</a>
<ul dir="auto">
<li><a href="#local-installation">Local Installation</a></li>
<li><a href="#gpu-version-cuda-for-windows-and-linux">GPU Version (CUDA) for Windows and Linux</a></li>
<li><a href="#setup-repository">Setup Repository</a></li>
</ul>
</li>
<li><a href="#usage">Usage</a>
<ul dir="auto">
<li><a href="#download-datasets">Download Datasets</a></li>
<li><a href="#training-models">Training Models</a></li>
<li><a href="#testing-models">Testing Models</a></li>
<li><a href="#using-instanseg-for-inference">Using InstanSeg for inference</a></li>
<li><a href="#model-versioning">Model versioning</a></li>
</ul>
</li>
</ul>
<div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Installing using pip</h2><a id="user-content-installing-using-pip" class="anchor" aria-label="Permalink: Installing using pip" href="#installing-using-pip"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<p dir="auto">For a minimal installation:</p>
<div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="pip install instanseg-torch"><pre>pip install instanseg-torch</pre></div>
<p dir="auto">if you want all the requirements used for training:</p>
<div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="pip install instanseg-torch[full]"><pre>pip install instanseg-torch[full]</pre></div>
<p dir="auto">You can get started immediately by calling the InstanSeg class:</p>
<div class="highlight highlight-source-python notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="from instanseg import InstanSeg
instanseg_brightfield = InstanSeg(&quot;brightfield_nuclei&quot;, image_reader= &quot;tiffslide&quot;, verbosity=1)

labeled_output = instanseg_brightfield.eval(image = &quot;../instanseg/examples/HE_example.tif&quot;,
                                            save_output = True,
                                            save_overlay = True)"><pre><span class="pl-k">from</span> <span class="pl-s1">instanseg</span> <span class="pl-k">import</span> <span class="pl-v">InstanSeg</span>
<span class="pl-s1">instanseg_brightfield</span> <span class="pl-c1">=</span> <span class="pl-en">InstanSeg</span>(<span class="pl-s">"brightfield_nuclei"</span>, <span class="pl-s1">image_reader</span><span class="pl-c1">=</span> <span class="pl-s">"tiffslide"</span>, <span class="pl-s1">verbosity</span><span class="pl-c1">=</span><span class="pl-c1">1</span>)

<span class="pl-s1">labeled_output</span> <span class="pl-c1">=</span> <span class="pl-s1">instanseg_brightfield</span>.<span class="pl-c1">eval</span>(<span class="pl-s1">image</span> <span class="pl-c1">=</span> <span class="pl-s">"../instanseg/examples/HE_example.tif"</span>,
                                            <span class="pl-s1">save_output</span> <span class="pl-c1">=</span> <span class="pl-c1">True</span>,
                                            <span class="pl-s1">save_overlay</span> <span class="pl-c1">=</span> <span class="pl-c1">True</span>)</pre></div>
<p dir="auto">Alternatively, if you want more control over the intermediate steps:</p>
<div class="highlight highlight-source-python notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="image_array, pixel_size = instanseg_brightfield.read_image(&quot;../instanseg/examples/HE_example.tif&quot;)

labeled_output, image_tensor  = instanseg_brightfield.eval_small_image(image_array, pixel_size)

display = instanseg_brightfield.display(image_tensor, labeled_output)

from instanseg.utils.utils import show_images
show_images(image_tensor,display, colorbar=False, titles = [&quot;Normalized Image&quot;, &quot;Image with segmentation&quot;])"><pre><span class="pl-s1">image_array</span>, <span class="pl-s1">pixel_size</span> <span class="pl-c1">=</span> <span class="pl-s1">instanseg_brightfield</span>.<span class="pl-c1">read_image</span>(<span class="pl-s">"../instanseg/examples/HE_example.tif"</span>)

<span class="pl-s1">labeled_output</span>, <span class="pl-s1">image_tensor</span>  <span class="pl-c1">=</span> <span class="pl-s1">instanseg_brightfield</span>.<span class="pl-c1">eval_small_image</span>(<span class="pl-s1">image_array</span>, <span class="pl-s1">pixel_size</span>)

<span class="pl-s1">display</span> <span class="pl-c1">=</span> <span class="pl-s1">instanseg_brightfield</span>.<span class="pl-c1">display</span>(<span class="pl-s1">image_tensor</span>, <span class="pl-s1">labeled_output</span>)

<span class="pl-k">from</span> <span class="pl-s1">instanseg</span>.<span class="pl-s1">utils</span>.<span class="pl-s1">utils</span> <span class="pl-k">import</span> <span class="pl-s1">show_images</span>
<span class="pl-en">show_images</span>(<span class="pl-s1">image_tensor</span>,<span class="pl-s1">display</span>, <span class="pl-s1">colorbar</span><span class="pl-c1">=</span><span class="pl-c1">False</span>, <span class="pl-s1">titles</span> <span class="pl-c1">=</span> [<span class="pl-s">"Normalized Image"</span>, <span class="pl-s">"Image with segmentation"</span>])</pre></div>
<div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Local Installation</h3><a id="user-content-local-installation" class="anchor" aria-label="Permalink: Local Installation" href="#local-installation"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<p dir="auto">To install InstanSeg locally, follow these steps:</p>
<ol dir="auto">
<li>
<p dir="auto">Install either Anaconda, Mamba, or <a href="https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html" rel="nofollow">micromamba</a>. We use micromamba for speed and simplicity, but you can replace "micromamba" with the distribution you are using.</p>
</li>
<li>
<p dir="auto">In your terminal or Anaconda prompt on Windows, create a new environment and install dependencies using the provided <code>env.yml</code> file:</p>
<div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="micromamba create -n instanseg --file env.yml"><pre>micromamba create -n instanseg --file env.yml</pre></div>
</li>
<li>
<p dir="auto">Activate your environment:</p>
<div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="micromamba activate instanseg"><pre>micromamba activate instanseg</pre></div>
</li>
</ol>
<div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">GPU Version (CUDA) for Windows and Linux</h3><a id="user-content-gpu-version-cuda-for-windows-and-linux" class="anchor" aria-label="Permalink: GPU Version (CUDA) for Windows and Linux" href="#gpu-version-cuda-for-windows-and-linux"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<p dir="auto">If you intend to use GPU acceleration and CUDA, follow these additional steps:</p>
<ol start="4" dir="auto">
<li>
<p dir="auto">Uninstall existing PyTorch and reinstall with CUDA support:</p>
<div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="micromamba remove pytorch torchvision monai
micromamba install pytorch==2.1.1 torchvision==0.16.1 monai=1.3.0 pytorch-cuda=12.1 -c conda-forge -c pytorch -c nvidia
pip install cupy-cuda12x"><pre>micromamba remove pytorch torchvision monai
micromamba install pytorch==2.1.1 torchvision==0.16.1 monai=1.3.0 pytorch-cuda=12.1 -c conda-forge -c pytorch -c nvidia
pip install cupy-cuda12x</pre></div>
</li>
<li>
<p dir="auto">Check if CUDA is available:</p>
<div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="python -c &quot;import torch; print('CUDA is available') if torch.cuda.is_available() else print('CUDA is not available')&quot;"><pre>python -c <span class="pl-s"><span class="pl-pds">"</span>import torch; print('CUDA is available') if torch.cuda.is_available() else print('CUDA is not available')<span class="pl-pds">"</span></span></pre></div>
</li>
</ol>
<p dir="auto">The repository may work with older versions of CUDA. For this replace "12.1" and "12" with the required version.</p>
<div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Setup Repository</h3><a id="user-content-setup-repository" class="anchor" aria-label="Permalink: Setup Repository" href="#setup-repository"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<ol start="3" dir="auto">
<li>Build repository:
<div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="pip install -e ."><pre>pip install -e <span class="pl-c1">.</span></pre></div>
</li>
</ol>
<div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Usage</h2><a id="user-content-usage" class="anchor" aria-label="Permalink: Usage" href="#usage"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Download Datasets</h3><a id="user-content-download-datasets" class="anchor" aria-label="Permalink: Download Datasets" href="#download-datasets"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<p dir="auto">To download public datasets and example images, follow the instructions under <strong>instanseg/notebooks/load_datasets.ipynb</strong></p>
<p dir="auto">To train InstanSeg on your own dataset, extend the <strong>instanseg/notebooks/load_datasets.ipynb</strong> with one of the templates provided.</p>
<div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Training Models</h3><a id="user-content-training-models" class="anchor" aria-label="Permalink: Training Models" href="#training-models"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<p dir="auto">To train models using InstanSeg, use the <strong>train.py</strong> script under the scripts folder.</p>
<p dir="auto">For example, to train InstanSeg on the TNBC_2018 dataset over 250 epochs at a pixel resolution of 0.25 microns/pixel, run the following command:</p>
<div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="cd instanseg/scripts
python train.py -data segmentation_dataset.pth -source &quot;[TNBC_2018]&quot; --num_epochs 250 --experiment_str my_first_instanseg --requested_pixel_size 0.25"><pre><span class="pl-c1">cd</span> instanseg/scripts
python train.py -data segmentation_dataset.pth -source <span class="pl-s"><span class="pl-pds">"</span>[TNBC_2018]<span class="pl-pds">"</span></span> --num_epochs 250 --experiment_str my_first_instanseg --requested_pixel_size 0.25</pre></div>
<p dir="auto">To train a channel invariant InstanSeg on the CPDMI_2023 dataset, predicting both nuclei and cells, run the following command:</p>
<div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="cd instanseg/scripts
python train.py -data segmentation_dataset.pth -source &quot;[CPDMI_2023]&quot; --num_epochs 250 --experiment_str my_first_instanseg -target NC --channel_invariant True --requested_pixel_size 0.5"><pre><span class="pl-c1">cd</span> instanseg/scripts
python train.py -data segmentation_dataset.pth -source <span class="pl-s"><span class="pl-pds">"</span>[CPDMI_2023]<span class="pl-pds">"</span></span> --num_epochs 250 --experiment_str my_first_instanseg -target NC --channel_invariant True --requested_pixel_size 0.5</pre></div>
<p dir="auto">Each epoch should take approximately 1 to 3 minutes to complete (with mps or cuda support).</p>
<p dir="auto">For more options and configurations, refer to the parser arguments in the train.py file.</p>
<div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Testing Models</h3><a id="user-content-testing-models" class="anchor" aria-label="Permalink: Testing Models" href="#testing-models"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<p dir="auto">To test trained models and obtain F1 metrics, use the following command:</p>
<div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="python test.py --model_folder my_first_instanseg -test_set Validation --optimize_hyperparameters True
python test.py --model_folder my_first_instanseg -test_set Test --params best_params"><pre>python test.py --model_folder my_first_instanseg -test_set Validation --optimize_hyperparameters True
python test.py --model_folder my_first_instanseg -test_set Test --params best_params</pre></div>
<div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Using InstanSeg for inference</h3><a id="user-content-using-instanseg-for-inference" class="anchor" aria-label="Permalink: Using InstanSeg for inference" href="#using-instanseg-for-inference"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="python inference.py --model_folder my_first_instanseg --image_path ../examples"><pre>python inference.py --model_folder my_first_instanseg --image_path ../examples</pre></div>
<p dir="auto">Replace "../examples" with the path to your images. If InstanSeg cannot read the image pixel size from the image metadata, the user is required to provide a --pixel_size parameter. InstanSeg provides (limited) support for whole slide images (WSIs). For more options and configurations, refer to the parser arguments in the inference.py file.</p>
<div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Model versioning</h3><a id="user-content-model-versioning" class="anchor" aria-label="Permalink: Model versioning" href="#model-versioning"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div>
<p dir="auto">Links to different model versions are stored in <code>instanseg/models/model-index.json</code>. When releasing new models,
you should add entries to this JSON file, optionally removing any previous versions that shouldn't be available in future versions.</p>
<p dir="auto">An example entry looks like this:</p>
<div class="highlight highlight-source-json notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="{
  &quot;name&quot;: &quot;[MODEL_NAME]&quot;,
  &quot;url&quot;: &quot;https://github.com/instanseg/instanseg/releases/download/[RELEASE_NAME]/[MODEL_NAME].zip&quot;,
  &quot;version&quot;: &quot;0.1.0&quot;,
  &quot;license&quot;: &quot;Apache-2.0&quot;
}"><pre>{
  <span class="pl-ent">"name"</span>: <span class="pl-s"><span class="pl-pds">"</span>[MODEL_NAME]<span class="pl-pds">"</span></span>,
  <span class="pl-ent">"url"</span>: <span class="pl-s"><span class="pl-pds">"</span>https://github.com/instanseg/instanseg/releases/download/[RELEASE_NAME]/[MODEL_NAME].zip<span class="pl-pds">"</span></span>,
  <span class="pl-ent">"version"</span>: <span class="pl-s"><span class="pl-pds">"</span>0.1.0<span class="pl-pds">"</span></span>,
  <span class="pl-ent">"license"</span>: <span class="pl-s"><span class="pl-pds">"</span>Apache-2.0<span class="pl-pds">"</span></span>
}</pre></div>
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      <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copy js-clipboard-copy-icon">
    <path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"></path><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path>
</svg>
      <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check js-clipboard-check-icon color-fg-success d-none">
    <path d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"></path>
</svg>
    </clipboard-copy>
  </div>
</template>




    </div>

    <div id="js-global-screen-reader-notice" class="sr-only mt-n1" aria-live="polite" aria-atomic="true" ></div>
    <div id="js-global-screen-reader-notice-assertive" class="sr-only mt-n1" aria-live="assertive" aria-atomic="true"></div>
  </body>
</html>

