mehta-lab/VisCy

Issues

• Document representation evaluation functions

  #177 opened 3 months ago by ziw-liu
  5

• Add a method ignore certain wells for training/validation

  #205 opened 25 days ago by edyoshikun
  0

• OOM issues with 3D FCMAE fine-tuning

  #201 opened a month ago by edyoshikun
  2

• Implement NT-Xent loss (implicit negative samples)

  #136 opened 4 months ago by ziw-liu
  3

• Investigate kvikio

  #199 opened a month ago by ziw-liu
  0

• Update `predict_writer` for iohub> 0.2.0

  #173 opened 2 months ago by edyoshikun
  0

• Add PCA to prediction of contrastive models

  #191 opened 2 months ago by ziw-liu
  0

• Store dimensionality reduction for feature visualization

  #166 opened 2 months ago by ziw-liu
  4

• Layer-wise learning rate decay during fine-tuning

  #75 opened 8 months ago by ziw-liu
  0

• WIP: refactor contrastive learning code with virtual staining code

  #109 opened 2 months ago by mattersoflight
  7

• organize application scripts on GitHub rather than disk

  #98 opened 5 months ago by mattersoflight
  0

• CLI for multiple training tasks

  #127 opened 2 months ago by mattersoflight
  4

• Number of UMAP components

  #165 opened 2 months ago by ziw-liu
  3

• Time sampling for positive pair

  #123 opened 2 months ago by alishbaimran
  0

• Support python 3.13

  #187 opened 2 months ago by ziw-liu
  1

• Update hosted virtual staining config files for 0.3.0

  #183 opened 2 months ago by ziw-liu
  1

• Move to NumPy style docstrings?

  #133 opened 4 months ago by ziw-liu
  1

• explainability tools for representation

  #157 opened 3 months ago by mattersoflight
  1

• Log embeddings in TensorBoard

  #155 opened 3 months ago by ziw-liu
  1

• Viscy workflow questions and experience from DL@MBL

  #52 opened a year ago by edyoshikun
  0

• document published models on Wiki

  #117 opened 3 months ago by mattersoflight
  2

• Update the projection head (normalization and size).

  #139 opened 3 months ago by mattersoflight
  4

• Contrastive Learning Implementation

  #90 opened 3 months ago by alishbaimran
  1

• Hard-coded stem stride in `ContrastiveEncoder`

  #138 opened 3 months ago by ziw-liu
  1

• Illustrative test datasets

  #101 opened 3 months ago by arteys
  5

• update the paths to video on readme

  #152 opened 3 months ago by edyoshikun
  2

• image translation exercise for DL@MBL

  #82 opened 3 months ago by mattersoflight
  2

• Patches with cells not in center

  #142 opened 3 months ago by Soorya19Pradeep
  3

• Unify stem implementation

  #120 opened 4 months ago by ziw-liu
  3

• Implement test time augmentations to avoid high frequency fluctuations

  #77 opened 4 months ago by mattersoflight
  1

• Normalization for patches ome-zarr

  #97 opened 4 months ago by alishbaimran
  2

• Model size mismatch error during prediction

  #134 opened 4 months ago by Soorya19Pradeep
  3

• Support loading data from a specific resolution of a .zarr pyramid

  #125 opened 4 months ago by talonchandler
  1

• switching to tensorboard logger for organelle phenotyping

  #116 opened 4 months ago by mattersoflight
  0

• Overflow error seen in training and prediction steps

  #110 opened 5 months ago by Soorya19Pradeep
  0

• API for 2D UNeXt2 model construction needs clarity

  #107 opened 5 months ago by mattersoflight
  2

• Predict module not giving expected output

  #102 opened 5 months ago by Soorya19Pradeep
  3

• VS predictions should output the correct voxel_size/scale

  #62 opened 5 months ago by edyoshikun
  2

• Compatibility issues

  #83 opened 6 months ago by ziw-liu
  10

• Three channel output using covnext model

  #78 opened 6 months ago by Soorya19Pradeep
  18

• Variable input size training and data pooling

  #65 opened 8 months ago by ziw-liu
  0

• clean up viscy cli display

  #73 opened 9 months ago by mattersoflight
  0

• upgrading lightning to >2.0.8 results to trainer issues

  #72 opened 9 months ago by edyoshikun
  4

• Citation for the Mantis paper

  #63 opened a year ago by ziw-liu
  1

• configurable augmentations

  #55 opened a year ago by mattersoflight
  1

• sample['target'] from a dataloader batch returns the wrong z-shape

  #47 opened a year ago by edyoshikun
  1

• documentation of data.py

  #48 opened a year ago by mattersoflight
  0

• Testing the training pipeline

  #56 opened a year ago by ziw-liu
  0

• strategies to improve invariance with data augmentation

  #54 opened a year ago by mattersoflight
  1

• Configure sample image logging during training

  #46 opened a year ago by ziw-liu
  0