Ecosyste.ms: Issues

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GitHub / hci-unihd/plant-seg issues and pull requests

#194 - Transfer PlantSeg from HCI to Kreshuk Lab

Issue - State: open - Opened by qin-yu 10 months ago - 3 comments

#193 - Rename generic plant nuclear model for paper submission

Pull Request - State: closed - Opened by qin-yu 10 months ago - 1 comment
Labels: enhancement

#192 - Generic plant nuclei model should be found as `PlantSeg_3Dnuc_platinum`

Issue - State: closed - Opened by qin-yu 10 months ago
Labels: enhancement

#191 - Redirect all Wiki links to new doc and improve READMEs

Pull Request - State: closed - Opened by qin-yu 10 months ago - 1 comment
Labels: documentation

#190 - Strong tiling artifacts

Issue - State: open - Opened by Buglakova 10 months ago

#188 - No instructions for how to do proofreading

Issue - State: closed - Opened by Buglakova 10 months ago - 1 comment
Labels: duplicate

#187 - Links in Docs and README still point to Wiki

Issue - State: closed - Opened by qin-yu 10 months ago - 2 comments
Labels: documentation

#185 - Only PlantSeg v1.6.0 available on conda-forge

Issue - State: open - Opened by qin-yu 10 months ago - 3 comments
Labels: bug

#184 - Fix Flow in GUI & Napari: key, channel, LMC in GUI; multi-channel UNet layers in Napari

Pull Request - State: closed - Opened by qin-yu 10 months ago - 4 comments
Labels: enhancement

#183 - Add the correct prediction channels in napari interface

Issue - State: closed - Opened by Buglakova 10 months ago - 1 comment
Labels: bug, enhancement

#181 - Wiki doc path update on python API

Issue - State: closed - Opened by jackyko1991 11 months ago - 1 comment
Labels: bug, documentation

#180 - Update mamba install

Pull Request - State: closed - Opened by jackyko1991 11 months ago - 3 comments

#179 - Add documentation folder and Actions for https://hci-unihd.github.io/plant-seg/

Pull Request - State: closed - Opened by qin-yu 11 months ago - 5 comments
Labels: documentation, enhancement

#178 - Fix multiple generic issues

Pull Request - State: open - Opened by lorenzocerrone 12 months ago

#177 - Update documentation

Issue - State: open - Opened by wolny 12 months ago - 9 comments
Labels: documentation

#176 - Move plantseg to conda-forge

Issue - State: closed - Opened by wolny 12 months ago - 9 comments

#174 - Add foreground/background postprocessing

Issue - State: open - Opened by wolny 12 months ago
Labels: enhancement

#173 - Support for GUI dataset/channel selection, follow #165

Issue - State: closed - Opened by qin-yu 12 months ago - 5 comments
Labels: enhancement

#172 - PlantSeg latest version, having issue with using CUDA from GUI.

Issue - State: closed - Opened by athulrv 12 months ago - 4 comments

#171 - PyQT is not installed automatically, can't run napari interface

Issue - State: open - Opened by Buglakova about 1 year ago - 2 comments

#170 - Add option to set home_path via PLANTSEG_HOME env-variable.

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

#169 - Add Zenodo record for generic plant nuclei model

Pull Request - State: closed - Opened by qin-yu about 1 year ago - 2 comments
Labels: enhancement

#168 - Error after updating plantseg

Issue - State: closed - Opened by athulrv about 1 year ago - 12 comments

#167 - update plantseg

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

#165 - Backward compatible `key` & `channel` params for config pipeline

Pull Request - State: closed - Opened by qin-yu about 1 year ago - 4 comments
Labels: enhancement

#164 - could not run GASP clustering on napari ver

Issue - State: closed - Opened by tats53 about 1 year ago

#161 - Add training and dataset managemnt

Pull Request - State: open - Opened by lorenzocerrone over 1 year ago

#160 - Ensure compatibility with models trained with pytorch-3dunet

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

#159 - Add support for training

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

#158 - instructions on training models

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

#157 - support for passing dataset keys for Zarr files

Issue - State: open - Opened by Mohinta2892 over 1 year ago

#156 - export of models in BioImage Model Zoo format

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

#155 - No compression for saving TIFF file

Issue - State: closed - Opened by qin-yu over 1 year ago - 1 comment
Labels: enhancement

#153 - `create_tiff()` changes the input numpy array, which may cause problems

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

#152 - Running plantseg segmentation algorithms on terabyte-scale images

Issue - State: closed - Opened by Mohinta2892 over 1 year ago - 1 comment

#151 - Add zarr support

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

#150 - Read write zarrs

Pull Request - State: closed - Opened by Mohinta2892 over 1 year ago

#149 - Add nice widgets callbacks

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

#148 - Better models names

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

#147 - Improve batch_size selection

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

#146 - AssertionError: Sample size has to be bigger than the patch size

Issue - State: open - Opened by lorenzocerrone over 1 year ago - 1 comment
Labels: enhancement

#145 - Notify if a new plantseg release is out

Issue - State: open - Opened by lorenzocerrone over 1 year ago - 3 comments
Labels: enhancement

#144 - Move plantseg to a new channel

Issue - State: closed - Opened by lorenzocerrone over 1 year ago - 2 comments
Labels: enhancement, question

#143 - reading zarrs

Issue - State: closed - Opened by Mohinta2892 over 1 year ago - 6 comments
Labels: enhancement

#142 - Better model selection

Issue - State: closed - Opened by wolny over 1 year ago - 5 comments
Labels: enhancement

#141 - Remove pytorch-3dunet dependency

Pull Request - State: closed - Opened by wolny over 1 year ago - 10 comments

#140 - Add support for multi-channel network output

Issue - State: closed - Opened by wolny over 1 year ago - 1 comment
Labels: enhancement

#139 - Fix incorrect model weights on Zenodo

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

#138 - Confocal Ovules ds2x and ds3x are the same

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

#137 - Minor UI improvements

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

#136 - Error during layer export

Issue - State: closed - Opened by wolny over 1 year ago - 5 comments
Labels: bug

#135 - Move models to zenodo

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

#134 - More stable and manteinable upload/download location for models

Issue - State: closed - Opened by lorenzocerrone over 1 year ago - 1 comment
Labels: question

#133 - Add corrected segmented mask to proofreading

Issue - State: closed - Opened by lorenzocerrone over 1 year ago
Labels: enhancement

#132 - Improved proofreading

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

#130 - Remove pytorch-3dunet dependency from plantseg

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

#129 - Replace 2D networks by a more efficient version

Issue - State: closed - Opened by wolny over 1 year ago
Labels: enhancement

#128 - Fix striding issues during prediction

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

#127 - Errors with PlantSeg implementation

Issue - State: open - Opened by upasana99 over 1 year ago - 6 comments

#126 - Cleanup documentation python api

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

#125 - New napari GUI is awesome!

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

#124 - Minor improvements

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

#123 - yaml.scanner.ScannerError: mapping values are not allowed here

Issue - State: open - Opened by e-tomato almost 2 years ago - 1 comment

#122 - Conda install needs specific Python version to work

Issue - State: closed - Opened by qin-yu almost 2 years ago - 1 comment

#121 - Problem running plant-seg on batch mode

Issue - State: open - Opened by lcferme about 2 years ago - 2 comments
Labels: question

#120 - Launching plant-seg after installation

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

#119 - fix conda pack bat on windows

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

#118 - Update LiftedMulticut with nucleus segmentation

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

#117 - Update LiftedMulticut with nucleus segmentation

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

#115 - start documentation migration to wiki

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

#114 - Input_paths cannot be empty

Issue - State: closed - Opened by ZH-GAO over 2 years ago - 3 comments

#113 - 2D segmentation of root meristem

Issue - State: closed - Opened by AlexStroh-git over 2 years ago - 2 comments
Labels: question

#112 - Windows binaries distribution

Pull Request - State: closed - Opened by lorenzocerrone almost 3 years ago - 1 comment

#111 - Move wget download requests

Pull Request - State: closed - Opened by lorenzocerrone almost 3 years ago

#110 - Move wget download requests

Pull Request - State: closed - Opened by lorenzocerrone almost 3 years ago

#109 - using nuclear probabilities or segmentations from StarDist

Issue - State: closed - Opened by pr4deepr almost 3 years ago - 11 comments
Labels: bug

#108 - Run plant-seg GUI and set either "Save Raw Data" on causes error

Issue - State: closed - Opened by qin-yu almost 3 years ago - 2 comments
Labels: bug

#107 - GASP doesn't work with nifty 1.2.1

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

#105 - Homogenize super pixel implementation for all workflows

Pull Request - State: closed - Opened by lorenzocerrone almost 3 years ago

#104 - fix bug in lmc

Pull Request - State: closed - Opened by lorenzocerrone almost 3 years ago

#101 - no nifty=1.0.9 for Win64 as of Oct '21

Issue - State: closed - Opened by Mrc010 about 3 years ago - 2 comments

#94 - evaluation

Issue - State: closed - Opened by soans1994 over 3 years ago - 2 comments

#83 - conda recipe problems

Issue - State: closed - Opened by lorenzocerrone over 3 years ago - 2 comments

#79 - New file structure for pipeline execution

Issue - State: closed - Opened by wolny over 3 years ago

#75 - AssertionError: Not enough patch overlap for stride

Issue - State: closed - Opened by e-tomato over 3 years ago - 2 comments
Labels: bug

#69 - Installation instructions don't work

Issue - State: closed - Opened by constantinpape over 3 years ago - 3 comments

#68 - PlantSeg Crashes before finishing predictions for each slice

Issue - State: closed - Opened by ellapenny over 3 years ago

#50 - [WIP] Initial work

Pull Request - State: closed - Opened by boykovdn over 4 years ago - 1 comment

#45 - Plantseg REST API

Pull Request - State: closed - Opened by wolny over 4 years ago - 1 comment