Issues

• Installation issues: pytorch version?

  computational-cell-analytics/micro-sam#1320 · Filter by author haesleinhuepf opened on Aug 6, 2026
  2

• Feature request: Add existing Labels layers as SAM mask inputs

  computational-cell-analytics/micro-sam#1315 · Filter by author arthursw opened on Jul 31, 2026

• Installing with uv complains about Python version missmatch

  computational-cell-analytics/micro-sam#1275 · Filter by author jo-mueller opened on Jul 2, 2026
  7

• Huggingface integration

  computational-cell-analytics/micro-sam#1136 · Filter by author constantinpape opened on Dec 23, 2025

• Troubles using checkpoint file to headlessly run inference on unseen data (unpickling errors?)

  computational-cell-analytics/micro-sam#1132 · Filter by author evaknichols opened on Dec 18, 2025
  6

• Improve the example finetuning notebook

  enhancement
  computational-cell-analytics/micro-sam#1118 · Filter by author constantinpape opened on Oct 23, 2025
  3

  

• Disable the premature optimization on writing z-slices

  enhancement
  computational-cell-analytics/micro-sam#1117 · Filter by author constantinpape opened on Oct 23, 2025

• Installing micro-sam headless

  computational-cell-analytics/micro-sam#1113 · Filter by author ElpadoCan opened on Sep 26, 2025
  13

• Feedback on object classification

  computational-cell-analytics/micro-sam#1100 · Filter by author anwai98 opened on Aug 25, 2025
  1

• Model documentation updates

  enhancement
  computational-cell-analytics/micro-sam#1099 · Filter by author constantinpape opened on Aug 20, 2025
  2

  

• Allow using PEFT (e.g. LoRA) in mask decoder with frozen image encoder

  computational-cell-analytics/micro-sam#1089 · Filter by author YonghaoZhao722 opened on Aug 2, 2025
  6

• Installation problems via windows installer

  computational-cell-analytics/micro-sam#1071 · Filter by author klmarina opened on Jun 19, 2025
  12

• Exporting to ONNX

  enhancementhelp wanted
  computational-cell-analytics/micro-sam#1062 · Filter by author ShreyasFadnavis opened on Jun 11, 2025
  2

• Incorporate and test instance-only / semantic-only training in CLI

  computational-cell-analytics/micro-sam#1025 · Filter by author anwai98 opened on May 9, 2025 · 1.6.1
  1

  

• Some doc updates

  documentation
  computational-cell-analytics/micro-sam#1011 · Filter by author constantinpape opened on Apr 22, 2025 · 1.6.1

• AttributeError: function 'FTC_CMapCache_Lookup' not found

  duplicate
  computational-cell-analytics/micro-sam#1007 · Filter by author z-pan opened on Apr 18, 2025
  2

• Implement saving tracking results to CTC format

  enhancement
  computational-cell-analytics/micro-sam#1006 · Filter by author constantinpape opened on Apr 17, 2025 · 1.6.1
  2

  

• Edits to current_object are sometimes lost on commit

  computational-cell-analytics/micro-sam#995 · Filter by author psobolewskiPhD opened on Apr 9, 2025
  1

• Weird results in interactive segmentation in batch mode with negative prompts

  computational-cell-analytics/micro-sam#977 · Filter by author constantinpape opened on Mar 28, 2025 · 1.6.1

• Follow-up on improvement ideas from TiM2025

  enhancement
  computational-cell-analytics/micro-sam#958 · Filter by author anwai98 opened on Mar 24, 2025

• Tracking integration

  computational-cell-analytics/micro-sam#906 · Filter by author constantinpape opened on Feb 28, 2025 · 1.6.1
  1

• Rebuild installers for windows and linux

  computational-cell-analytics/micro-sam#888 · Filter by author anwai98 opened on Feb 24, 2025 · 1.6.1
  1

• Documentation for scaling-up micro_sam to Whole Slide Images

  computational-cell-analytics/micro-sam#875 · Filter by author fercer opened on Feb 20, 2025
  1

• Add support for (optional) preprocessing of inputs

  enhancement
  computational-cell-analytics/micro-sam#870 · Filter by author anwai98 opened on Feb 20, 2025 · 1.6.1
  1

  

• Feature request: allow segmentation to work when axes are reordered, e.g. orthogonal view

  enhancement
  computational-cell-analytics/micro-sam#805 · Filter by author psobolewskiPhD opened on Nov 29, 2024
  5