Ecosyste.ms: Issues

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GitHub / mehta-lab/VisCy issues and pull requests

#56 - Testing the training pipeline

Issue - State: open - Opened by ziw-liu over 1 year ago

#55 - configurable augmentations

Issue - State: closed - Opened by mattersoflight over 1 year ago - 1 comment

#54 - strategies to improve invariance with data augmentation

Issue - State: open - Opened by mattersoflight over 1 year ago - 1 comment

#53 - Visualize feature maps

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

#52 - Viscy workflow questions and experience from DL@MBL

Issue - State: open - Opened by edyoshikun over 1 year ago

#51 - Fix center slice metrics for 3D output

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

#50 - Document data methods

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

#49 - Configure the number of image samples logged at each epoch and batch

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

#48 - documentation of data.py

Issue - State: closed - Opened by mattersoflight over 1 year ago
Labels: documentation

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

Issue - State: closed - Opened by edyoshikun over 1 year ago - 1 comment
Labels: bug

#46 - Configure sample image logging during training

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

#45 - Example workflow

Pull Request - State: closed - Opened by ziw-liu over 1 year ago - 4 comments
Labels: documentation

#44 - dlmbl 2023 archive

Pull Request - State: closed - Opened by mattersoflight over 1 year ago

#43 - Clarify how to use different stages of VisCy

Issue - State: closed - Opened by edyoshikun over 1 year ago - 3 comments
Labels: documentation

#42 - architectures and nomenculature

Issue - State: closed - Opened by mattersoflight over 1 year ago - 6 comments

#41 - Update readme.md typo for `cd VisCy`

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

#40 - Unable to load two channesl as inputs to do fluoresence to phase image translation

Issue - State: closed - Opened by edyoshikun over 1 year ago - 1 comment
Labels: bug

#39 - viscy -> VisCy (#34)

Pull Request - State: closed - Opened by mattersoflight over 1 year ago

#38 - Project icon

Pull Request - State: closed - Opened by ziw-liu over 1 year ago - 12 comments
Labels: documentation, enhancement

#37 - 2.1D upscale decoder

Pull Request - State: closed - Opened by ziw-liu over 1 year ago - 4 comments

#36 - DLMBL 2023 excercise

Pull Request - State: closed - Opened by ziw-liu over 1 year ago - 3 comments

#35 - Allow sampling multiple patches from the same stack

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

#34 - viscy -> VisCy

Pull Request - State: closed - Opened by mattersoflight over 1 year ago

#33 - PSNR as a regression metric

Issue - State: closed - Opened by ziw-liu over 1 year ago - 3 comments
Labels: enhancement

#32 - Fix inference

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

#31 - Improve augmentation

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

#30 - readme + dependencies tested with python 3.10

Pull Request - State: closed - Opened by mattersoflight over 1 year ago

#29 - Demo notebooks

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

#28 - Fix datamodule

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

#27 - 3D augmentation and 2.1D U-Net

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

#26 - draft demo dataset and notebook

Issue - State: closed - Opened by mattersoflight over 1 year ago - 2 comments

#25 - Bump iohub version

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

#24 - sampling strategy to improve class balance across cell cycle

Issue - State: open - Opened by mattersoflight over 1 year ago - 1 comment

#23 - Augmentation strategy for mantis data

Issue - State: closed - Opened by ziw-liu over 1 year ago - 5 comments

#22 - Update README

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

#21 - Test metrics

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

#20 - Save augmented tiles

Issue - State: closed - Opened by JohannaRahm almost 3 years ago - 2 comments

#19 - Discussion of what metrics to prioritize in inference tensorboard

Issue - State: closed - Opened by Christianfoley almost 2 years ago - 4 comments

#18 - Inference output image format

Issue - State: closed - Opened by Soorya19Pradeep almost 2 years ago - 7 comments

#17 - Does phase input need to be normalized with dataset statistics?

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 4 comments

#16 - Augmentation strategy for generalization across magnification

Issue - State: open - Opened by ziw-liu almost 2 years ago - 1 comment

#14 - Multi-channel training and prediction

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

#13 - Cleanup torch module registration

Issue - State: open - Opened by ziw-liu over 1 year ago

#12 - Update CI and code QA

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

#11 - Keep segmentation task for U-Nets?

Issue - State: closed - Opened by ziw-liu over 1 year ago - 2 comments

#10 - Upgrade MONAI

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

#9 - ONNX export CLI

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

#8 - Update docs

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

#7 - Packaging the project

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

#6 - Remove outdated scripts

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

#5 - Cleanup

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

#4 - Test framework

Issue - State: closed - Opened by ziw-liu over 1 year ago - 3 comments

#3 - Code for aligning Z focus

Issue - State: closed - Opened by ziw-liu over 1 year ago - 2 comments

#2 - Rename the micro_dl module to viscy

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

#1 - Migration from microDL

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