yuqiyuqitan/SPACEc

Issues

• Tissue_segmentation - Noise removal

  #63 opened 2 days ago by dtejadam
  0

• catplot zoom

  #61 opened 7 days ago by talban14
  1

• Cell assignments in qupath

  #62 opened 7 days ago by talban14
  1

• Run container on High Performance computing cluster (HPC)

  #60 opened a month ago by ryao-mdanderson
  3

• Windows installation instructions

  #59 opened a month ago by bobbyni819
  3

• Compare Spatial context maps and motifs

  #58 opened a month ago by Zach-Sten
  1

• omp_set_nested routine deprecated

  #57 opened 2 months ago by dtejadam
  0

• Not able to download data from Dryad

  #56 opened 2 months ago by pranjalvaidya
  1

• sp.hf.downscale_tissue does not recognize the tissue pieces

  #55 opened 2 months ago by dtejadam
  4

• Mac M1/M2 error

  #54 opened 4 months ago by fotisn7
  1

• Duplicated code in filter_interactions

  #29 opened 4 months ago by TKempchen
  0

• import issue: Windows x64 ModuleNotFoundError: No module named '_libvips'

  #53 opened 4 months ago by yuqiyuqitan
  1

• FYI: this project requires CUDA 11

  #52 opened 4 months ago by aowenson-imm
  3

• `import spacec` took over 60mins but eventually caused kernel Python 3.9 die on M1

  #51 opened 4 months ago by denvercal1234GitHub
  1

• `pytest` produced Interrupted: 42 errors during collection

  #50 opened 5 months ago by denvercal1234GitHub
  1

• Using StarDist cell segmentation within SPACEc?

  #46 opened 5 months ago by denvercal1234GitHub
  4

• Installation for Mac M1

  #47 opened 5 months ago by denvercal1234GitHub
  3

• werkzeug error on Apple M1/M2/M3 when loading SPACEc

  #49 opened 5 months ago by TKempchen
  0

• fastremap error when installing SPACEc on Apple M1/M2/M3

  #48 opened 5 months ago by TKempchen
  0

• `scanpy` is currently fixed on 1.9.6 since tests don't run otherwise

  #18 opened 5 months ago by mgbckr
  0

• Notebook 4 is missing the code to generate barycentric coordinate system

  #20 opened 5 months ago by TKempchen
  0

• Unstable Github Actions

  #25 opened 5 months ago by mgbckr
  2

• Tutorial page coming soon?

  #45 opened 5 months ago by denvercal1234GitHub
  3

• Release TODOs

  #26 opened 5 months ago by mgbckr
  0

• CPU vs GPU installation

  #32 opened 5 months ago by yuqiyuqitan
  0

• Add Setup.ipynb

  #14 opened 5 months ago by TKempchen
  1

• Python 3.11 does not work because of DeepCell which requires Python <= 3.10

  #16 opened 5 months ago by mgbckr
  0

• Mesmer Segmentation works has issues with 32bit files users should reduce to 16 or 8bit for segmentation input

  #22 opened 5 months ago by TKempchen
  0

• Change text font size for create_pie_charts

  #31 opened 6 months ago by yuqiyuqitan
  0

• Decide how we would like to handle plot saving

  #10 opened 6 months ago by TKempchen
  0

• M1/M2 fix is hacky

  #23 opened 9 months ago by mgbckr
  0

• `sp.tl.identify_interactions` fails on Windows due to `joblib` issue in Github action tests

  #19 opened 10 months ago by mgbckr
  3

• Make tests run via Github Actions

  #17 opened 9 months ago by mgbckr
  3

• Plotting functions save

  #7 opened 10 months ago by TKempchen
  1

• Fix fragmented functions

  #8 opened 10 months ago by TKempchen
  2

• Normalization in pl_swarm_box function does not work correctly

  #9 opened 10 months ago by TKempchen
  1

• We have an unclear thresholding procedure for the CN maps

  #13 opened 10 months ago by TKempchen
  0

• functions that need to get rid of the module note

  #15 opened 10 months ago by yuqiyuqitan
  1

• Tensor decomposition not working

  #5 opened 10 months ago by TKempchen
  1

• Remove R scripts from Repo

  #12 opened 10 months ago by TKempchen
  0

• generalize "pl_membrane_ch" and "tl_cell_segmentation" function

  #11 opened 10 months ago by TKempchen
  0

• Barycentric coordinate system

  #4 opened a year ago by TKempchen
  1

• Decide on common color theme

  #6 opened a year ago by TKempchen
  0

• CCA not working

  #3 opened a year ago by TKempchen
  0