fmi-basel/gliberal-scMultipleX

Issues

• Update scmultiplex README

  #121 opened 4 months ago by jluethi
  0

• Handle np.float deprecation

  #104 opened 5 months ago by jluethi
  2

• Not depending on `fractal-tasks-core[fractal-tasks]` may introduce import errors

  #113 opened 5 months ago by tcompa
  2

• Cannot install with pip 24.1

  #106 opened 6 months ago by tcompa
  3

• Test measurements for tiny objects

  #101 opened a year ago by jluethi
  1

• Optional saving of relabelled and transformed images (task 3)

  #93 opened a year ago by nrepina
  0

• Save affine and ffd transformation to file

  #95 opened a year ago by enricotagliavini
  0

• Check PlatyMatch parallelization

  #88 opened a year ago by nrepina
  0

• Add choice of affine or affine+ffd to config file (task 3)

  #92 opened a year ago by nrepina
  0

• Bug in plot_image_grid plotting function

  #100 opened a year ago by nrepina
  0

• Max wishlist

  #97 opened a year ago by nrepina
  0

• Add illumination correction option

  #47 opened a year ago by nrepina
  0

• Output euclidian distances before transformation in run_affine function

  #89 opened a year ago by nrepina
  0

• Improve logging when user makes input mistake in scmpx Fractal task

  #84 opened a year ago by nrepina
  4

• Support masked ROI loading in Fractal task

  #80 opened 2 years ago by jluethi
  0

• Measurement bug in 3D Fractal measurements

  #79 opened 2 years ago by jluethi
  2

• Skeleton features

  #78 opened 2 years ago by MauriceKahnwald
  0

• Refactor nuclear linking code to share processing functions with Fractal

  #76 opened 2 years ago by nrepina
  0

• Add PlatyMatch license file

  #75 opened 2 years ago by nrepina
  0

• Refactor organoid linking

  #70 opened 2 years ago by nrepina
  0

• Enhance nuclear linking exception handling

  #73 opened 2 years ago by enricotagliavini
  0

• Clean up logging for missing segmentations during feature extraction

  #26 opened 2 years ago by nrepina
  1

• Make separate logger for scmultiplex tasks

  #30 opened 2 years ago by nrepina
  2

• Clean up common config

  #45 opened 2 years ago by nrepina
  1

• Remove ovr_channel parameter since it is the same as org_seg_channel param

  #27 opened 2 years ago by nrepina
  0

• Check for scikit-image version and apply the fix for centroid for version 0.20.0

  #69 opened 2 years ago by enricotagliavini
  0

• Fractal task adds duplicate columns

  #67 opened 2 years ago by jluethi
  0

• Remove TODO.md?

  #56 opened 2 years ago by enricotagliavini
  1

• Maurice wish list of features

  #23 opened 2 years ago by nrepina
  0

• Add neighbor analysis to FeatureExtraction.py

  #64 opened 2 years ago by nrepina
  1

• Testing of different experiment settings

  #63 opened 2 years ago by nrepina
  0

• Cleanup the get_regionprops_measurements() function in feature_wrapper.py

  #59 opened 2 years ago by enricotagliavini
  3

• Bundle faim_hcs v0.1.1?

  #52 opened 2 years ago by enricotagliavini
  0

• Fix typos

  #43 opened 2 years ago by nrepina
  0

• Make --config option mandatory in all prefect scripts

  #32 opened 2 years ago by enricotagliavini
  0

• Add version info to scMpx log file output

  #48 opened 2 years ago by nrepina
  0

• Check if output is correct of regionprops Z weighted_centroid

  #53 opened 2 years ago by nrepina
  1

• Fix incomplete rows in Feature extraction

  #51 opened 2 years ago by enricotagliavini
  7

• Print summary at the end of nuc to mem linking

  #58 opened 2 years ago by enricotagliavini
  0

• Two Z centroids: scaled and unscaled

  #55 opened 2 years ago by nrepina
  0

• Add support for cluster submission

  #31 opened 2 years ago by enricotagliavini
  0

• Add a check for step dependencies ?

  #34 opened 2 years ago by enricotagliavini
  0

• Make surface area measurement optional

  #28 opened 2 years ago by nrepina
  0

• Change naming of Aspect Ration feature to be more specific

  #50 opened 2 years ago by nrepina
  0

• More testing for 01 task parallelization

  #46 opened 2 years ago by enricotagliavini
  0

• Return non zero exit code when a Flow is no successful

  #40 opened 2 years ago by enricotagliavini
  1

• Check and error out if config file doesn't exists

  #42 opened 2 years ago by enricotagliavini
  1

• Find solution for failure of multiprocessing in task 02

  #36 opened 2 years ago by nrepina
  1

• Add disconnected component detection for both 2D and 3D images (during featx)

  #24 opened 2 years ago by nrepina
  0

• Separate organoid feature extraction into C01 (shape) vs. other ch features

  #25 opened 2 years ago by nrepina
  0