mehta-lab/VisCy issues and pull requests

#156 - Module and scripts for evaluating representations

Pull Request - State: open - Opened by mattersoflight 5 months ago

#155 - Log embeddings in TensorBoard

Issue - State: open - Opened by ziw-liu 5 months ago - 1 comment
Labels: enhancement

#154 - Sample positive and negative samples with a time offset for the triplet contrastive task

Pull Request - State: open - Opened by ziw-liu 5 months ago
Labels: enhancement

#153 - Single-cell representation learning (dev)

Pull Request - State: open - Opened by ziw-liu 6 months ago
Labels: bug, enhancement, breaking

#152 - update the paths to video on readme

Issue - State: closed - Opened by edyoshikun 6 months ago - 2 comments
Labels: documentation

#151 - Fix deprecated custom forward method

Pull Request - State: closed - Opened by ziw-liu 6 months ago
Labels: maintenance

#150 - Remove obsolete scripts for contrastive phenotyping

Pull Request - State: closed - Opened by ziw-liu 6 months ago - 1 comment
Labels: maintenance

#149 - updating the notebook after running it at DLMBL2024

Pull Request - State: open - Opened by edyoshikun 6 months ago - 2 comments
Labels: documentation

#148 - Compbio demo

Pull Request - State: open - Opened by mattersoflight 6 months ago

#147 - Simultaneously plot tracks in latent space and real space

Pull Request - State: closed - Opened by mattersoflight 6 months ago - 1 comment

#146 - Merging code related to figures

Pull Request - State: closed - Opened by mattersoflight 6 months ago

#145 - SSL: fix MLP head and remove L2 normalization

Pull Request - State: closed - Opened by ziw-liu 6 months ago - 2 comments
Labels: bug, enhancement, breaking

#144 - Add script to visualize effective receptive field

Pull Request - State: open - Opened by ziw-liu 6 months ago
Labels: documentation

#143 - Use new AMP custom forward API

Pull Request - State: closed - Opened by ziw-liu 6 months ago - 2 comments
Labels: maintenance

#142 - Patches with cells not in center

Issue - State: closed - Opened by Soorya19Pradeep 6 months ago - 3 comments

#141 - SSL: fix MLP head and remove L2 normalization

Pull Request - State: closed - Opened by mattersoflight 6 months ago - 5 comments
Labels: bug, enhancement, breaking

#140 - produce a report of useful visualizations to assess the dimensionality and features learned by embeddings

Pull Request - State: closed - Opened by mattersoflight 6 months ago

#139 - Update the projection head (normalization and size).

Issue - State: open - Opened by mattersoflight 6 months ago - 3 comments

#138 - Hard-coded stem stride in `ContrastiveEncoder`

Issue - State: closed - Opened by ziw-liu 6 months ago - 1 comment
Labels: bug

#137 - Animated latent space

Pull Request - State: closed - Opened by ziw-liu 6 months ago

#136 - Implement NT-Xent loss (implicit negative samples)

Issue - State: open - Opened by ziw-liu 6 months ago - 2 comments
Labels: enhancement

#135 - Plot tracks in latent space and real space

Pull Request - State: closed - Opened by mattersoflight 6 months ago - 3 comments

#134 - Model size mismatch error during prediction

Issue - State: closed - Opened by Soorya19Pradeep 6 months ago - 3 comments

#133 - Move to NumPy style docstrings?

Issue - State: open - Opened by ziw-liu 6 months ago - 1 comment
Labels: documentation, maintenance

#132 - Config-based prediction with Xarray-based output format

Pull Request - State: closed - Opened by ziw-liu 6 months ago - 4 comments
Labels: enhancement

#131 - Configurable drop path rate in contrastive models

Pull Request - State: closed - Opened by ziw-liu 6 months ago - 1 comment
Labels: enhancement

#130 - Updated code (contrastive learning)

Pull Request - State: closed - Opened by alishbaimran 6 months ago

#129 - Adding support for pyramids

Pull Request - State: open - Opened by edyoshikun 6 months ago - 3 comments
Labels: enhancement

#128 - version lighting CLI example

Pull Request - State: closed - Opened by mattersoflight 6 months ago - 2 comments
Labels: documentation

#127 - CLI for multiple training tasks

Issue - State: open - Opened by mattersoflight 6 months ago - 4 comments

#126 - Tune augmentations with CLI and config for contrastive models

Pull Request - State: closed - Opened by ziw-liu 6 months ago - 3 comments
Labels: enhancement

#125 - Support loading data from a specific resolution of a .zarr pyramid

Issue - State: open - Opened by talonchandler 6 months ago - 1 comment
Labels: enhancement

#124 - Merge updated training w/ tb logging

Pull Request - State: closed - Opened by alishbaimran 6 months ago - 4 comments

#123 - Time sampling for positive pair

Issue - State: open - Opened by alishbaimran 6 months ago

#122 - Migrate from wandb to tensorboard

Pull Request - State: closed - Opened by ziw-liu 6 months ago - 1 comment

#121 - Update prediction in contrastive phenotyping

Pull Request - State: closed - Opened by ziw-liu 6 months ago

#120 - Unify stem implementation

Issue - State: closed - Opened by ziw-liu 6 months ago - 3 comments
Labels: maintenance

#119 - Adding link to demos and library of VS models wiki

Pull Request - State: closed - Opened by edyoshikun 6 months ago - 2 comments

#118 - Infection state

Pull Request - State: closed - Opened by alishbaimran 7 months ago - 1 comment

#117 - document published models on Wiki

Issue - State: open - Opened by mattersoflight 7 months ago - 1 comment
Labels: documentation

#116 - switching to tensorboard logger for organelle phenotyping

Issue - State: closed - Opened by mattersoflight 7 months ago

#115 - fixed the stem and forward pass

Pull Request - State: closed - Opened by mattersoflight 7 months ago

#114 - DLMBL 2024 notebook

Pull Request - State: closed - Opened by edyoshikun 7 months ago - 3 comments
Labels: documentation

#113 - Single-cell phenotyping with contrastive learning

Pull Request - State: closed - Opened by ziw-liu 7 months ago - 2 comments
Labels: enhancement

#112 - Update demo setup script

Pull Request - State: closed - Opened by ziw-liu 7 months ago - 1 comment
Labels: documentation

#111 - Pin numpy due to MONAI bug

Pull Request - State: closed - Opened by ziw-liu 7 months ago - 1 comment
Labels: maintenance

#110 - Overflow error seen in training and prediction steps

Issue - State: closed - Opened by Soorya19Pradeep 7 months ago
Labels: maintenance

#109 - WIP: refactor contrastive learning code with virtual staining code

Issue - State: open - Opened by mattersoflight 7 months ago - 6 comments

#108 - Adding segmentation utility functions

Pull Request - State: open - Opened by edyoshikun 7 months ago

#107 - API for 2D UNeXt2 model construction needs clarity

Issue - State: open - Opened by mattersoflight 7 months ago - 2 comments

#106 - HTML to markdown

Pull Request - State: closed - Opened by ziw-liu 7 months ago

#105 - Bump lightning and matplotlib

Pull Request - State: closed - Opened by ziw-liu 7 months ago
Labels: maintenance

#104 - add resnet50 to ContrastiveEncoder

Pull Request - State: closed - Opened by duopeng 7 months ago

#103 - Update dataset URL for demos

Pull Request - State: closed - Opened by ziw-liu 7 months ago
Labels: documentation

#102 - Predict module not giving expected output

Issue - State: closed - Opened by Soorya19Pradeep 7 months ago - 3 comments

#101 - Illustrative test datasets

Issue - State: closed - Opened by arteys 7 months ago - 5 comments
Labels: question

#100 - Updating demo notebook for training

Pull Request - State: closed - Opened by edyoshikun 7 months ago - 1 comment
Labels: documentation

#99 - Contrastive_dataloader

Pull Request - State: closed - Opened by mattersoflight 7 months ago

#98 - organize application scripts on GitHub rather than disk

Issue - State: open - Opened by mattersoflight 8 months ago

#97 - Normalization for patches ome-zarr

Issue - State: closed - Opened by alishbaimran 8 months ago - 2 comments

#96 - README update

Pull Request - State: closed - Opened by ziw-liu 8 months ago - 6 comments
Labels: documentation

#95 - Fix demos on other platforms

Pull Request - State: closed - Opened by ziw-liu 8 months ago - 4 comments
Labels: bug, documentation

#94 - Demo for VSCyto2D and VSCyto3D

Pull Request - State: closed - Opened by edyoshikun 8 months ago - 1 comment
Labels: documentation

#93 - Scale metadata handling for positions

Pull Request - State: closed - Opened by edyoshikun 8 months ago

#92 - bumping to cellpose 3

Pull Request - State: closed - Opened by edyoshikun 8 months ago

#91 - Test time augmentations

Pull Request - State: closed - Opened by edyoshikun 8 months ago - 2 comments
Labels: enhancement

#90 - Contrastive Learning Implementation

Issue - State: open - Opened by alishbaimran 8 months ago - 1 comment
Labels: enhancement

#89 - Add the scale metadata to the output_stores

Pull Request - State: closed - Opened by edyoshikun 8 months ago - 1 comment
Labels: enhancement

#88 - Test on Python 3.12

Pull Request - State: closed - Opened by ziw-liu 8 months ago
Labels: maintenance, CI

#87 - Test on Python 3.12

Pull Request - State: closed - Opened by ziw-liu 8 months ago - 2 comments
Labels: maintenance, CI

#86 - Fix architecture name in network diagram script

Pull Request - State: closed - Opened by ziw-liu 8 months ago - 1 comment
Labels: bug

#85 - Add preprint reference to README

Pull Request - State: closed - Opened by ziw-liu 8 months ago - 1 comment
Labels: documentation

#84 - Rename UNeXt2

Pull Request - State: closed - Opened by ziw-liu 8 months ago - 2 comments
Labels: documentation

#83 - Compatibility issues

Issue - State: closed - Opened by ziw-liu 8 months ago - 10 comments

#82 - image translation exercise for DL@MBL

Issue - State: closed - Opened by mattersoflight 8 months ago - 2 comments

#81 - Test time agumentations

Pull Request - State: closed - Opened by edyoshikun 8 months ago - 1 comment

#80 - Fix 3D to 2D prediction with UNeXt2 model

Pull Request - State: closed - Opened by ziw-liu 9 months ago - 1 comment

#79 - Add CITATION.cff

Pull Request - State: closed - Opened by ziw-liu 9 months ago

#78 - Three channel output using covnext model

Issue - State: closed - Opened by Soorya19Pradeep 9 months ago - 18 comments
Labels: help wanted

#77 - Implement test time augmentations to avoid high frequency fluctuations

Issue - State: closed - Opened by mattersoflight 9 months ago - 1 comment

#76 - solution notebook

Pull Request - State: closed - Opened by esgomezm 9 months ago - 1 comment

#75 - Layer-wise learning rate decay during fine-tuning

Issue - State: open - Opened by ziw-liu 10 months ago
Labels: enhancement

#74 - Filter empty detections in labels

Pull Request - State: closed - Opened by ziw-liu 10 months ago
Labels: bug

#73 - clean up viscy cli display

Issue - State: open - Opened by mattersoflight 11 months ago
Labels: documentation

#72 - upgrading lightning to >2.0.8 results to trainer issues

Issue - State: closed - Opened by edyoshikun 11 months ago - 4 comments

#71 - 2D FCMAE

Pull Request - State: closed - Opened by ziw-liu 11 months ago

#70 - Cellular infection phenotyping using annotated viral sensor data & label-free images

Pull Request - State: closed - Opened by Soorya19Pradeep 11 months ago - 5 comments
Labels: enhancement

#69 - Test on python 3.12

Pull Request - State: closed - Opened by ziw-liu 12 months ago - 2 comments
Labels: maintenance, CI

#68 - configurable normalizations

Pull Request - State: closed - Opened by edyoshikun 12 months ago - 1 comment

#67 - Masked autoencoder pre-training for virtual staining models

Pull Request - State: closed - Opened by ziw-liu about 1 year ago - 3 comments
Labels: enhancement

#66 - checkpoint as a model config parameter for warmup cosine learning rates

Pull Request - State: closed - Opened by edyoshikun about 1 year ago

#65 - Variable input size training and data pooling

Issue - State: closed - Opened by ziw-liu about 1 year ago
Labels: enhancement

#64 - Bump dependencies and update documentation

Pull Request - State: closed - Opened by ziw-liu about 1 year ago
Labels: documentation, maintenance, CI

#63 - Citation for the Mantis paper

Issue - State: closed - Opened by ziw-liu about 1 year ago - 1 comment

#62 - VS predictions should output the correct voxel_size/scale

Issue - State: closed - Opened by edyoshikun about 1 year ago - 2 comments
Labels: enhancement

#61 - Configurable augmentations

Pull Request - State: closed - Opened by ziw-liu about 1 year ago - 1 comment
Labels: enhancement

#60 - Example script for parsing CLI config files in Python

Pull Request - State: closed - Opened by ziw-liu over 1 year ago - 1 comment
Labels: documentation

#59 - Preprocess CLI and source scaling during prediction

Pull Request - State: closed - Opened by ziw-liu over 1 year ago - 1 comment
Labels: enhancement

#58 - Baseline 3D-LUNeXt

Pull Request - State: closed - Opened by ziw-liu over 1 year ago - 1 comment

#57 - Fix predicting new channels in an existing store

Pull Request - State: closed - Opened by ziw-liu over 1 year ago
Labels: bug

GitHub / mehta-lab/VisCy issues and pull requests