axondeepseg/axondeepseg

Issues

• Change installation procedure to SCT/ST-style shell script install

  #820 opened 2 months ago by mathieuboudreau
  0

• Consolidate two Coveralls reporting APIs

  #818 opened 2 months ago by mathieuboudreau
  0

• Clarify `segment_folders()` fn behavior

  #813 opened 3 months ago by hermancollin
  3

• Extension to Palmgren Silver Images

  #817 opened 2 months ago by abadgerw
  3

• Add mandatory preprocessing steps before inference

  #805 opened 4 months ago by hermancollin
  1

• Morphometrics computation for perimeter doesn't reflect outermost perimeter

  #776 opened 10 months ago by hermancollin
  10

• Auto-fill models into our ReadTheDocs/Sphinx for auto-update

  #811 opened 3 months ago by mathieuboudreau
  3

• axondeepseg does not work on python 3.12 as of June 2024.

  #807 opened 4 months ago by dccote
  1

• Handle PIP - archive or delete?

  #808 opened 4 months ago by mathieuboudreau
  0

• our `imread` and `imwrite` are barely tested

  #806 opened 4 months ago by hermancollin
  1

• Refactor CLI options for nnunet

  #798 opened 5 months ago by hermancollin
  2

• Should we remove `ads_plugin.py`?

  #804 opened 4 months ago by hermancollin
  3

• [napari plugin] Display better information in case there is an error

  #802 opened 4 months ago by Stoyan-I-A
  0

• Fresh `git clone` is ~150MB due to large files in git history

  #793 opened 6 months ago by joshuacwnewton
  8

• Add MODEL CARDS (list of all models + detailed description)

  #799 opened 5 months ago by hermancollin
  0

• Adapt download_model script to fetch release assets

  #797 opened 6 months ago by hermancollin
  1

• Segment nerve section to compute axon density

  #782 opened 8 months ago by hermancollin
  2

• download_models could use a little makeover

  #717 opened 5 months ago by hermancollin
  5

• Support unmyelinated axons in morphometrics

  #795 opened 5 months ago by hermancollin
  9

• Re-train ivadomed models with nnUNet

  #771 opened 5 months ago by hermancollin
  8

• Add "myelin cutter" model for postprocessing

  #768 opened 6 months ago by hermancollin
  17

• Add GUI gif in README

  #791 opened 7 months ago by hermancollin
  3

• Error during Windows install

  #789 opened 7 months ago by Eddymorphling
  12

• Unused data on OSF

  #787 opened 7 months ago by hermancollin
  0

• Axon Discrimination for QC

  #786 opened 7 months ago by hermancollin
  0

• Add Quality Assurance features

  #760 opened a year ago by mathieuboudreau
  3

• Output morphometric file and histogram PNGs of key metrics (eg axon diameter, myelin thickness, g-ratio) with every segmentation run.

  #779 opened 9 months ago by mathieuboudreau
  0

• 16 bit tifs not converted properly to 8 bit when images are loaded

  #737 opened a year ago by mathieuboudreau
  14

• Bug: Image loaded "as gray" deprecated

  #738 opened 9 months ago by mathieuboudreau
  3

• Fine-tune SAM for axonmyelin segmentation on TEM dataset

  #770 opened a year ago by hermancollin
  0

• Create testimonials page

  #759 opened a year ago by jcohenadad
  13

• Add support for `nnunetv2` models

  #765 opened a year ago by hermancollin
  1

• Build fails due to onnxruntime update

  #757 opened a year ago by mathieuboudreau
  0

• Sciatic nerve toluidine blue image analysis on AxonDeepSeg

  #754 opened a year ago by apuer11
  7

• [napari plugin] "resampled size too low" message is not showing up

  #749 opened a year ago by Stoyan-I-A
  0

• How to change pixel size in napari

  #747 opened a year ago by hermancollin
  3

• Error trying to train models "raise source.error("bad escape %s" % escape, len(escape)) re.error: bad escape \m at position 10"

  #743 opened a year ago by GrimmSnark
  2

• Deprecated config_to_csv.py

  #718 opened a year ago by hermancollin
  1

• Installation failing on Windows

  #733 opened a year ago by mathieuboudreau
  3

• Add tooltips to Napari buttons

  #731 opened 2 years ago by mathieuboudreau
  0

• Consider moving the config.py file inside the AxonDeepSeg directory.

  #724 opened 2 years ago by Stoyan-I-A
  0

• Train dataset with MONAI & compare segmentations with IVADOMED

  #722 opened 2 years ago by mathieuboudreau
  0

• File pull_request_template.md contains a dead link

  #719 opened 2 years ago by trallnag
  1

• Importing AxonDeepSeg.segment on its own creates an OpenMP error

  #716 opened 2 years ago by Stoyan-I-A
  6

• Remove openCV dependency

  #712 opened 2 years ago by Stoyan-I-A
  0

• Wiki cleanup

  #715 opened 2 years ago by hermancollin
  1

• 16-bit images cannot be loaded

  #709 opened 2 years ago by hermancollin
  5

• Scheduled CI fails irregularly on Windows (no-patch test)

  #706 opened 2 years ago by mathieuboudreau
  6

• Problems opening fsleyes after ads_plugin.py

  #705 opened 2 years ago by djcvan
  3

• RAM limitations with no-patch option

  #703 opened 2 years ago by mariehbourget
  0