EliHei2/segger_dev

Issues

• [BUG] Docker + test data leads to create_anndata() error

  #76 opened in 12 hours
  4

• ValueError in LitSegger from tutorial

  #75 opened 12 hours ago
  5

• segger in COSMX data - data generation step

  #74 opened 12 hours ago
  3

• [Model Training] abrupt change in 'validation_f1'

  #70 opened a month ago
  3

• [Visualisation] Baysor-like output

  #69 opened a month ago
  2

• [BUG] ValueError while tuning parameters

  #68 opened 2 months ago
  1

• Adding obsm['spatial'] to anndata output from segger

  #65 opened 2 months ago
  0

• [BUG] attribute error while making predictions

  #62 opened 2 months ago
  4

• TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.

  #59 opened 3 months ago
  2

• [BUG] runtime error while making predictions

  #52 opened 3 months ago
  5

• [Documentation] Updating docs with new API and add tutorials for new functionalities.

  #50 opened 3 months ago
  0

• bug fix - numpy depreciation error.

  #49 opened 3 months ago
  0

• seg2explorer arguments

  #45 opened 3 months ago
  4

• Attribute error during dataset creation

  #43 opened 3 months ago
  1

• [BUG] duplicate test

  #35 opened 3 months ago
  2

• AttributeError: 'EdgeStorage' object has no attribute 'edge_label_index'

  #34 opened 3 months ago
  14

• Change cagra.build_index to cagra.build

  #33 opened 3 months ago
  2

• Segger Similarity Score Histogram

  #32 opened 2 months ago
  6

• 'pip install..' throws errors

  #29 opened 3 months ago
  4

• [BUG] If num_workers > 1, data processing skips a significant number of tiles.

  #27 opened 3 months ago
  7

• [BUG] Specifying tile_width and tile_height but not tile_size raises ValueError in STSampleParquet pipeline

  #25 opened 3 months ago
  2

• cell type abundance embedding

  #24 opened 2 months ago
  2

• `spatialdata` support in `segger`

  #20 opened 3 months ago
  2

• [BUG] `XeniumDataset` class imported in `segger.cli.predict` and `segger.cli.train_model`

  #19 opened 3 months ago
  0

• [BUG] Segger segment() crashes due to memory limits

  #17 opened 3 months ago
  1

• Add saving options for final segmentation

  #16 opened 3 months ago
  0

• Move setting embedding weights to Segger model initialization

  #15 opened 3 months ago
  0

• RAPIDS support discontinued for systems running OS versions lower than Ubuntu 20.04 or Rocky Linux 8

  #14 opened 3 months ago
  3

• Produce cell mask polygons and connect to bento-tools for post-hoc geometrical assessment

  #13 opened 3 months ago
  0

• Early stopping for training

  #12 opened 3 months ago
  0

• [BUG] Training fails on new Xenium Prime data format

  #11 opened 3 months ago
  0

• [BUG] TypeError in build_pyg_data_from_tile

  #10 opened 4 months ago
  5

• Segger installation troubles

  #9 opened 3 months ago
  10

• Connect Sopa and Segger

  #8 opened 3 months ago
  2