saeyslab/napari-sparrow

Issues

• Adapt code to Xenium data

  #97 opened 8 days ago by lopollar
  1

• fix the plot_control transcripts for large images

  #107 opened 17 days ago by lopollar
  2

• dpi parameter for plot functions

  #198 opened 5 months ago by lotte-vandevreken
  0

• enhance plot_shapes

  #104 opened a year ago by lopollar
  2

• Cannot add shapes layer to sdata from numpy array

  #182 opened 18 days ago by julienmortier
  4

• Possibility to add multiple Field of Views to one sdata object

  #125 opened 18 days ago by lopollar
  1

• Clean up experiments

  #116 opened 18 days ago by lopollar
  1

• labels to shapes function

  #184 opened 18 days ago by julienmortier
  3

• Bug in allocate_intensity, does segmentation

  #185 opened 18 days ago by berombau
  4

• Testing of output for the different plots

  #118 opened 18 days ago by SilverViking
  1

• Calculate average pixel brightness per segmented object

  #130 opened 18 days ago by lopollar
  4

• Installation on windows

  #176 opened 18 days ago by lopollar
  1

• Error in creating conda environment with .yml

  #200 opened 4 months ago by HeesooSong
  7

• Allocate step fails with "ValueError: negative dimensions are not allowed" on large stereoseq dataset

  #199 opened 4 months ago by SilverViking
  1

• Add Baysor for cell segmentation

  #96 opened 4 months ago by rseurinc
  3

• Split napari-sparrow into sparrow (pipeline only) and napari-sparrow (plugin only)?

  #122 opened 4 months ago by SilverViking
  1

• create_voronoi_boundaries() throws TopologyException

  #114 opened 4 months ago by SilverViking
  2

• Document code using docstrings

  #120 opened 4 months ago by SilverViking
  0

• Problem to install sparrow mesmer env

  #183 opened 7 months ago by Lucas-Maciel
  2

• Geometries when expanding don't save properly

  #187 opened 7 months ago by lopollar
  3

• View SpatialData object in napari-spatialdata

  #179 opened 8 months ago by ArneDefauw
  2

• KeyError: "'None' not found in sdata.images or sdata.labels"

  #171 opened 8 months ago by Lucas-Maciel
  2

• AttributeError: module 'numpy' has no attribute 'float'.

  #174 opened 9 months ago by julienmortier
  2

• AttributeError: module 'ml_dtypes' has no attribute 'float8_e4m3b11'

  #146 opened 9 months ago by Lucas-Maciel
  1

• pandas version 2.1.0

  #134 opened a year ago by ArneDefauw
  2

• Weird behaviour: size_min_max_filter

  #159 opened a year ago by KoenDesplenter
  5

• Refactor functions.py

  #121 opened a year ago by SilverViking
  1

• add the option to plot filtered out cells to main

  #129 opened a year ago by lopollar
  2

• tiling_correction "Reweighting did not converge" error

  #150 opened a year ago by sttimmer
  2

• Installation problems solved

  #133 opened a year ago by WoutVanhenden
  4

• Issues with installation of packages

  #131 opened a year ago by lopollar
  3

• Segmentation parameter min_size (for discarding small fragments) has no effect

  #128 opened a year ago by SilverViking
  1

• Clean up debug and logging messages

  #119 opened a year ago by SilverViking
  2

• take into account subset when analyzing genes filtered out

  #111 opened a year ago by lopollar
  3

• adapt tilingCorrection plot

  #105 opened a year ago by lopollar
  1

• Problem reading SpatialData on Windows

  #127 opened a year ago by julienmortier
  2

• Add minimum number of counts per cell and minimum number of cells per gene to napari UI

  #123 opened a year ago by julienmortier
  2

• Make it possible to restart at every step

  #99 opened a year ago by lopollar
  7

• make it possible to load in subset

  #110 opened a year ago by lopollar
  2

• problems with contrast enhancing

  #126 opened a year ago by lopollar
  1

• Code for Sankey plots

  #109 opened a year ago by lopollar
  1

• Tiling correction when image size is not multiple of tile size

  #113 opened a year ago by ArneDefauw
  2

• fix counts column in points layer plus allocation

  #117 opened a year ago by lopollar
  0

• Output how many transcripts are used

  #106 opened a year ago by lopollar
  1

• Find oud why overwriting is so slow

  #112 opened a year ago by lopollar
  1

• plot shapes of filtered out cells

  #108 opened a year ago by lopollar
  1

• Adapt code to BGI data

  #100 opened a year ago by lopollar
  1

• dask: make allocation possible

  #101 opened a year ago by lopollar
  1

• Add different types of gene allocation

  #98 opened a year ago by lopollar
  1

• add xarray plotting to notebooks

  #102 opened a year ago by lopollar
  1