nf-core/molkart

Issues

• Segmentation with Stardist

  #80 opened a month ago
  1

• Add methods description in report

  #79 opened a month ago
  0

• Fully move to nf-test

  #77 opened a month ago
  0

• Make Mindagap optional

  #74 opened 13 days ago
  0

• Optimize parameters for full test data

  #73 opened 4 months ago
  0

• MultiQC custom output

  #72 opened a month ago
  0

• nf-core/molkart template update 2.14.1

  #70 opened 4 months ago
  0

• Issue: Unable to run Ilastik with different image sizes.

  #69 opened 4 months ago
  0

• Fix create training set module to not create overlapping crops

  #68 opened 5 months ago
  0

• Benchmark & Improve Cellpose performance

  #67 opened 5 months ago
  0

• Update training image counts to start at 1 instead of 0

  #66 opened 5 months ago
  0

• Create training subset - uncouple hdf5 / tiff cropping

  #63 opened 7 months ago
  0

• Template update for nf-core/tools v2.13.1 in Molkart

  #62 opened 4 months ago
  0

• Unable to install cellpose with apptainer on HPC

  #61 opened 4 months ago
  4

• Replace Zenodo DOI with a general one (accidentally used the one only for 1.0.0)

  #59 opened 4 months ago
  0

• Deepcell_mesmer doesn't work on AWS with WAVE and FUSION

  #56 opened 4 months ago
  4

• Merge template update for nf-core/tools v2.11

  #47 opened 9 months ago
  0

• Mesmer randomly fails on HPC using singularity due to model loading

  #43 opened 9 months ago
  1

• Go over remaining TODOs

  #41 opened 9 months ago
  0

• Maskfilter too slow

  #38 opened 10 months ago
  1

• Update tower.yml to include all qc metrics

  #37 opened 8 months ago
  2

• Reduce image size for local modules.

  #34 opened 10 months ago
  1

• If create training subset is run, pass crop overview to MultiQC.

  #29 opened 10 months ago
  1

• Molcart_QC --> Molkart_QC

  #28 opened 10 months ago
  1

• Clahe optimization

  #27 opened 10 months ago
  2

• Add anndata container as an output format

  #26 opened 9 months ago
  1

• Documentation update

  #24 opened 10 months ago
  1

• Mesmer does not require stack

  #22 opened a year ago
  0

• Mindagap - multiple samples with same input name

  #21 opened a year ago
  0

• Additional parameters for Mindagap_mindagap and Mindagap_duplicatefinder

  #17 opened a year ago
  2

• Add tag to project_spots container / spot2cell container

  #16 opened 10 months ago
  2

• Replace clahe parameter to skip_clahe so that the default is set to False, not True

  #13 opened a year ago
  1

• Add testing using nf-test

  #12 opened 9 months ago
  4

• Replace project spots and mcquant with faster method

  #11 opened a year ago
  1

• Add QC parsing with MultiQC

  #9 opened a year ago
  2

• Add option to filter masks and exclude mean intensities

  #8 opened 10 months ago
  7

• #molkart QC parsing with MultiQC

  #7 opened a year ago
  0

• Add ilastik pixel classifier and multicut as segmentation options

  #6 opened a year ago
  1

• Documentation update: add documentation

  #5 opened a year ago
  1