Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / constantinpape/torch-em issues and pull requests

#147 - UNETR with SAM initialization is not working yet

Issue - State: open - Opened by constantinpape about 1 year ago

#146 - Implement UNETR

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

#145 - Update trainer.fit

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

#144 - Refactor experiments

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

#142 - Implement sponge em dataset

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

#141 - Implement Sponge Dataset

Issue - State: closed - Opened by constantinpape about 1 year ago

#140 - Implement DeePict Dataset

Issue - State: open - Opened by constantinpape about 1 year ago - 1 comment

#139 - Implement NucMM Dataset

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

#138 - Dataset updates

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

#137 - Implement get_dataset for more datasets

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

#136 - Update check_loader to save plots

Pull Request - State: closed - Opened by anwai98 about 1 year ago

#135 - Add deepbacs dataloader

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

#134 - TissueNet Dataloader

Pull Request - State: closed - Opened by anwai98 about 1 year ago

#133 - UNETR Implementation in torch-em

Pull Request - State: closed - Opened by anwai98 about 1 year ago - 2 comments

#132 - Update Teacher Initialization for MT Setup

Pull Request - State: closed - Opened by anwai98 over 1 year ago

#131 - Try to fix conda build issues

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

#130 - Implement tif support in data loaders

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

#129 - Update Prediction Functions for PUNet Domain Adaptation Setups

Pull Request - State: closed - Opened by anwai98 over 1 year ago

#128 - Add CLI for UNet training and prediction

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

#126 - Add FixMatch-based Probabilistic Domain Adaptation Setups

Pull Request - State: closed - Opened by anwai98 over 1 year ago

#125 - Add Probabilistic Self-Training (MT) Approaches

Pull Request - State: closed - Opened by anwai98 over 1 year ago

#124 - Check failing test

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

#123 - Add 2D Probabilistic UNet Training Setup

Pull Request - State: closed - Opened by anwai98 over 1 year ago - 1 comment

#122 - Update Evaluation with Distribution Alignment

Pull Request - State: closed - Opened by anwai98 over 1 year ago

#121 - Add Argument - Target Domain

Pull Request - State: closed - Opened by anwai98 over 1 year ago

#120 - Implement classification functionality

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

#119 - Add 2D Probabilistic UNet

Pull Request - State: closed - Opened by anwai98 over 1 year ago - 1 comment

#118 - Add all necessary tests for mean teacher trainer deserialization

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

#117 - Load utils

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

#116 - Update Mean-Teacher and FixMatch Self-Training Scheme(s)

Pull Request - State: closed - Opened by anwai98 over 1 year ago - 2 comments

#115 - Update Prob-DA Source UNet Parameters

Pull Request - State: closed - Opened by anwai98 over 1 year ago

#114 - New datasets and other changes

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

#113 - Add support for torch2

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

#112 - Implement MeanTeacher Trainer

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

#110 - Misc changes WIP

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

#109 - Update Checksum for UroCell Dataloader

Pull Request - State: closed - Opened by anwai98 over 1 year ago

#108 - add args to adjust tqdm output

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

#107 - add dense accumulate as additional baseline

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

#106 - Raise value error if dice is called with non-matching shapes

Pull Request - State: closed - Opened by constantinpape almost 2 years ago

#105 - Update Label Type Argument for LiveCELL

Pull Request - State: closed - Opened by anwai98 almost 2 years ago

#104 - Add Separate Label Path to the LiveCELL Loader

Pull Request - State: closed - Opened by anwai98 almost 2 years ago - 1 comment

#103 - Follow ups: SPOCO

Issue - State: open - Opened by constantinpape almost 2 years ago

#102 - ResNet3d updates

Issue - State: open - Opened by constantinpape almost 2 years ago

#101 - implement gradient masking with cropping - new PR

Pull Request - State: closed - Opened by JonasHell almost 2 years ago - 2 comments

#100 - Update livecell.py

Pull Request - State: closed - Opened by constantinpape almost 2 years ago

#99 - Add resnet 3d implementation (based on torchvision)

Pull Request - State: closed - Opened by constantinpape almost 2 years ago

#98 - Augmentations

Pull Request - State: closed - Opened by JonasHell almost 2 years ago

#97 - provide reasonable default values for augmentations

Pull Request - State: closed - Opened by JonasHell almost 2 years ago

#96 - Implement sampler for the image collection dataset

Pull Request - State: closed - Opened by constantinpape about 2 years ago

#95 - Multiple class output

Issue - State: open - Opened by Czaki about 2 years ago - 7 comments

#94 - When loading data for train allow to read data that has channel on first position

Pull Request - State: closed - Opened by Czaki about 2 years ago - 2 comments

#93 - Use tifffile to read compressed tif files

Pull Request - State: closed - Opened by Czaki about 2 years ago - 2 comments

#92 - Add support for multichannel compresed tif files

Issue - State: closed - Opened by Czaki about 2 years ago - 5 comments

#91 - Sample code from Readme ends with error

Issue - State: closed - Opened by Czaki about 2 years ago - 1 comment

#90 - implement gradient masking with cropping

Pull Request - State: closed - Opened by JonasHell about 2 years ago

#89 - fix bioimageio import in shallow2deep

Pull Request - State: closed - Opened by JonasHell about 2 years ago

#88 - Make bioimageio import optional

Pull Request - State: closed - Opened by constantinpape about 2 years ago

#87 - Update spoco losses

Pull Request - State: closed - Opened by constantinpape about 2 years ago - 1 comment

#86 - Use ApplyMask in other masking loss wrappers

Pull Request - State: closed - Opened by constantinpape about 2 years ago

#84 - Add distance transform to label transforms

Pull Request - State: closed - Opened by constantinpape about 2 years ago

#83 - adapt _serialize_feature_config() to work with strings

Pull Request - State: closed - Opened by JonasHell about 2 years ago

#82 - adapt default mean teacher augs to work with modelzoo export

Pull Request - State: closed - Opened by JonasHell about 2 years ago

#81 - More shallow2deep exp

Pull Request - State: open - Opened by constantinpape about 2 years ago

#80 - Add tests for augmentations

Pull Request - State: closed - Opened by constantinpape about 2 years ago - 1 comment

#79 - Elastic 3d

Pull Request - State: closed - Opened by Buglakova about 2 years ago - 1 comment

#78 - fix kwargs, other strategies have no img_shape

Pull Request - State: closed - Opened by JonasHell about 2 years ago - 1 comment

#77 - add worst_tiles sampling

Pull Request - State: closed - Opened by JonasHell about 2 years ago - 4 comments

#76 - Implement halo enlargment for transforms

Issue - State: open - Opened by constantinpape about 2 years ago

#75 - Extend s2d functionality

Pull Request - State: closed - Opened by constantinpape about 2 years ago

#74 - Add axon myelin training

Pull Request - State: closed - Opened by constantinpape about 2 years ago

#73 - fix typo/bug in validation logging

Pull Request - State: closed - Opened by JonasHell about 2 years ago

#72 - Implement resize augmentations

Issue - State: open - Opened by constantinpape about 2 years ago

#71 - S2D experiments for training LM enhancers

Pull Request - State: closed - Opened by constantinpape about 2 years ago

#70 - Add general functionality for resampling datasets

Issue - State: closed - Opened by constantinpape about 2 years ago - 1 comment

#69 - 2D-UNet training notebook doesn't work for Colab

Issue - State: closed - Opened by qin-yu about 2 years ago - 3 comments

#68 - add noise augmentations for mean teacher approach

Pull Request - State: closed - Opened by JonasHell about 2 years ago

#67 - Extend shallow2deep experiments

Pull Request - State: closed - Opened by constantinpape about 2 years ago

#65 - Enable overwriting the min-shape in modelzoo export

Pull Request - State: closed - Opened by constantinpape about 2 years ago

#64 - Update s2d features, extend mito-enhancer training

Pull Request - State: closed - Opened by constantinpape about 2 years ago

#63 - Implement advanced rf training for s2d

Pull Request - State: closed - Opened by constantinpape about 2 years ago

#62 - Add functionality to mask to-bg-boundaries

Pull Request - State: closed - Opened by JonasHell over 2 years ago

#61 - ensure correct behaviour of filters when set manually

Pull Request - State: closed - Opened by JonasHell over 2 years ago

#59 - fix typo in augmentations

Pull Request - State: closed - Opened by JonasHell over 2 years ago

#58 - Add s2d notebooks

Pull Request - State: open - Opened by constantinpape over 2 years ago

#57 - fix error connected to retain_grad()

Pull Request - State: closed - Opened by JonasHell over 2 years ago - 1 comment

#56 - Fix deserialization by applying RoiWrapper

Pull Request - State: closed - Opened by JonasHell over 2 years ago - 1 comment

#55 - Deserialize ROI Wrapper WIP

Pull Request - State: closed - Opened by constantinpape over 2 years ago - 1 comment

#54 - Add Serializer to DefaultTrainer

Pull Request - State: closed - Opened by FynnBe over 2 years ago

#53 - refactor DefaultTrainer.from_checkpoint

Pull Request - State: closed - Opened by FynnBe over 2 years ago - 3 comments

#52 - Expand tests for trainer

Pull Request - State: closed - Opened by constantinpape over 2 years ago - 1 comment

#51 - refactor _train_epoch and _validate

Pull Request - State: closed - Opened by FynnBe over 2 years ago

#50 - fix best_metric < worst_metric

Pull Request - State: closed - Opened by FynnBe over 2 years ago - 1 comment

#49 - Add training notebooks

Pull Request - State: closed - Opened by constantinpape over 2 years ago

#48 - Allow logger to generate a (run) id

Pull Request - State: closed - Opened by FynnBe over 2 years ago