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1. Commits on Jul 7, 2026

   • Update README.md

     MicheleBortol

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2. Commits on Jul 3, 2026

   • Revise README with updated file structure and links

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     MicheleBortol

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   • Remove get_example_data.sh from README structure

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3. Commits on Jul 1, 2026

   • Fixes discrepancy between cropped table and cell_boundaries

     MicheleBortol

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   • Removes unmerged protein and RNA tables

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   • Fixes plotting

     MicheleBortol

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4. Commits on Jun 29, 2026

   • Update README.md

     MicheleBortol

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5. Commits on Jun 26, 2026

   • Merge pull request #26 from scOpenLab/harpy

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   • Readds plotting and fixed example notebook

     MicheleBortol

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   • Merge pull request #25 from scOpenLab/harpy

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     MicheleBortol

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6. Commits on Jun 25, 2026

   • Adds protein quantification

     MicheleBortol

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   • Merge pull request #24 from scOpenLab/harpy

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     MicheleBortol

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   • Load and Register all MACSima channels at once.

     MicheleBortol

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7. Commits on Jun 24, 2026

   • Merge pull request #23 from scOpenLab/harpy

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     MicheleBortol

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   • Added harpy, crop with SpatialData

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8. Commits on Jun 23, 2026

   • Cleanup README

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   • Merge pull request #22 from scOpenLab/add_labels

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   • Adds cell_labels

     MicheleBortol

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9. Commits on Jun 19, 2026

   • Merge pull request #21 from scOpenLab/workflow_cleanup

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     MicheleBortol

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   • Fix boundaries, tables, registrations

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10. Commits on Jun 16, 2026

    • Merge pull request #19 from scOpenLab/workflow_cleanup

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      MicheleBortol

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    • workflow cleanup

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11. Commits on Jun 11, 2026

    • Merge pull request #16 from scOpenLab/workflow_cleanup

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    • Fix roi index plot

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    • Merge branch 'main' of https://github.com/scOpenLab/MACSimaXenium into workflow_cleanup

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    • Adds ROI map loading from csv file

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12. Commits on May 13, 2026

    • Add quantify markers

      JRosenbauer

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13. Commits on May 4, 2026

    • Update xenium mf loading, and cleanup

      MicheleBortol

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    • Merge branch 'Cindy_documentation_updates' of https://github.com/scOpenLab/MACSimaXenium

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    • Merge branch 'Cindy_documentation_updates' of https://github.com/scOpenLab/MACSimaXenium into workflow_cleanup

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14. Commits on Apr 30, 2026

    • Fix: created a new function _resolve_morphology_dapi_path that can either find v3 or v4 xenium ouput version of the morphology focused images (closes #8)

      cpulloa

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15. Commits on Apr 29, 2026

    • Merge pull request #15 from scOpenLab/plotting

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      MicheleBortol

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    • Merge branch 'main' of https://github.com/scOpenLab/MACSimaXenium into plotting

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    • Use create_registration_summary_plot for the QC plot.

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    • Use create_registration_summary_plot for the summary plots.

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