Issues

• Release tag for 3.1?

  ClearAnatomics/ClearMap#194 · Filter by author akesandgren opened on Aug 28, 2026

• [BUG]

  bug
  ClearAnatomics/ClearMap#193 · Filter by author bsatterw opened on Jul 14, 2026

• [BUG] GUI stitching fails for Blaze datasets (KeyError: 'Z' in Preview, ValueError: Z not in tile_axes=['X','Y'] in Run Stitching)

  bug
  ClearAnatomics/ClearMap#192 · Filter by author RedTabby01 opened on Jul 6, 2026

• [BUG] Software crashes when I click on "View Atlas"

  bug
  ClearAnatomics/ClearMap#191 · Filter by author bsatterw opened on Jun 11, 2026
  5

• How do I enable checkpointing or resume execution for the stitch_layout step?

  ClearAnatomics/ClearMap#188 · Filter by author liu-wq opened on Dec 25, 2025
  1

• Stats calculations not running on the GUI

  ClearAnatomics/ClearMap#185 · Filter by author microscopycore-ismms opened on Oct 21, 2025
  3

• Getting ValueError: Incompatible shapes (266, 395, 164) != (44, 65, 82) for the source Tif-Source(44, 65, 82)

  ClearAnatomics/ClearMap#182 · Filter by author michaelmell opened on Sep 11, 2025
  1

• [BUG] Cannot Create a ClearMap environment

  bug
  ClearAnatomics/ClearMap#179 · Filter by author garretttan23 opened on Jun 4, 2025
  1

• Using ClearMap on previously stitched images

  ClearAnatomics/ClearMap#170 · Filter by author alexjanis opened on Apr 3, 2025
  1

• Confusing Documents of Wobbly Stitcher

  ClearAnatomics/ClearMap#169 · Filter by author Chrisa142857 opened on Mar 30, 2025

• How to install in windows system

  ClearAnatomics/ClearMap#167 · Filter by author LaylaQAQ opened on Mar 25, 2025
  3

• Obtaining Information on Stitching from .lyt files

  ClearAnatomics/ClearMap#166 · Filter by author Tas-V opened on Mar 24, 2025

• could not connect to display

  ClearAnatomics/ClearMap#160 · Filter by author GimenaA opened on Feb 27, 2025
  1

• [BUG] Cannot find a valid transformation file in 'elastix_resampled_to_auto'

  bug
  ClearAnatomics/ClearMap#157 · Filter by author Mtkostecki opened on Feb 10, 2025

• Registration of one hemisphere

  ClearAnatomics/ClearMap#156 · Filter by author ved-sharma opened on Jan 29, 2025

• Running stitching with only 2 axes

  ClearAnatomics/ClearMap#155 · Filter by author lauhei opened on Jan 28, 2025
  2

• Using custom atlas in ClearMap GUI

  ClearAnatomics/ClearMap#154 · Filter by author dkutsovsky opened on Dec 19, 2024
  2

• [NEW_FEATURE] Allow faster graph loading when edge geometry is not needed

  enhancement
  ClearAnatomics/ClearMap#152 · Filter by author edoumazane opened on Nov 22, 2024
  

• [BUG] IO: Unable to read TIF file that was written by ClearMap (custom script)

  bug
  ClearAnatomics/ClearMap#151 · Filter by author edoumazane opened on Nov 21, 2024
  1

• Confusing stitch progress bar

  ClearAnatomics/ClearMap#150 · Filter by author Chrisa142857 opened on Sep 22, 2024
  1

• tuple index of range (resampling autofluorescence step)

  ClearAnatomics/ClearMap#149 · Filter by author c3rry opened on Sep 13, 2024

• Subclasses should implement this method

  ClearAnatomics/ClearMap#148 · Filter by author c3rry opened on Sep 9, 2024

• Z dimension not detected for preview rigid stitching

  ClearAnatomics/ClearMap#147 · Filter by author stellalessandra opened on Sep 9, 2024
  1

• ClearMap GUI missing "Run detection" button

  ClearAnatomics/ClearMap#146 · Filter by author ved-sharma opened on Aug 23, 2024
  1

• cannot import name 'Texture3D' from 'vispy.visuals.volume'

  ClearAnatomics/ClearMap#145 · Filter by author c3rry opened on Jul 23, 2024
  3