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kreshuklab
/
plant-seg
A tool for cell instance aware segmentation in densely packed 3D volumetric images
https://kreshuklab.github.io/plant-seg/
MIT License
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`statics_kwargs` vs `runtime_kwargs`
#208
qin-yu
opened
6 months ago
2
Add option to only run official models in "Try all Available Models"
#207
qin-yu
closed
6 months ago
0
`cudnn` needs to be installed for some systems
#206
qin-yu
closed
6 months ago
0
`patch_halo` seems to be ignored
#205
qin-yu
closed
5 months ago
6
No channel selection in "Open File" widget
#204
qin-yu
closed
5 months ago
2
No voxel size information on images saved from PlantSeg Napari GUI
#203
qin-yu
closed
6 months ago
1
Add widget: remove objects using a probability map
#202
qin-yu
closed
6 months ago
6
v1.6.5 crash on launch
#201
qin-yu
closed
6 months ago
0
It would be nice to know exactly which instances are removed by postprocessing steps
#200
qin-yu
opened
6 months ago
0
Napari UI: Coordinate doesn't reflect real position
#199
qin-yu
opened
6 months ago
0
Napari UI: Renamed layers no updated in dropdown lists
#198
qin-yu
opened
6 months ago
2
Need to change link to docs on conda-forge
#197
qin-yu
closed
6 months ago
0
Linux and Windows installation commands differ
#196
qin-yu
closed
6 months ago
2
No orthoviewer
#195
qin-yu
opened
6 months ago
1
Transfer PlantSeg from HCI to Kreshuk Lab
#194
qin-yu
closed
3 months ago
5
Rename generic plant nuclear model for paper submission
#193
qin-yu
closed
6 months ago
2
Generic plant nuclei model should be found as `PlantSeg_3Dnuc_platinum`
#192
qin-yu
closed
6 months ago
0
Redirect all Wiki links to new doc and improve READMEs
#191
qin-yu
closed
7 months ago
1
Strong tiling artifacts
#190
Buglakova
closed
4 months ago
3
Help to choose the correct scale to apply the network
#189
Buglakova
opened
7 months ago
2
No instructions for how to do proofreading
#188
Buglakova
closed
7 months ago
1
Links in Docs and README still point to Wiki
#187
qin-yu
closed
7 months ago
2
Erosion option for nuclei channel in Lifted MultiCut and Segmentation Fix in Extra-Seg
#186
qin-yu
opened
7 months ago
0
Only PlantSeg v1.6.0 available on conda-forge
#185
qin-yu
closed
6 months ago
5
Fix Flow in GUI & Napari: key, channel, LMC in GUI; multi-channel UNet layers in Napari
#184
qin-yu
closed
7 months ago
4
Add the correct prediction channels in napari interface
#183
Buglakova
closed
7 months ago
1
Workaround to run plant-seg in colaboratory (with CUDA12.2 as of Jan. 2024)
#182
totti0223
closed
3 months ago
2
Wiki doc path update on python API
#181
jackyko1991
closed
8 months ago
1
Update mamba install
#180
jackyko1991
closed
7 months ago
3
Add documentation folder and Actions for https://hci-unihd.github.io/plant-seg/
#179
qin-yu
closed
8 months ago
5
Fix multiple generic issues
#178
lorenzocerrone
opened
8 months ago
0
Video tutorials
#177
wolny
opened
9 months ago
11
Move plantseg to conda-forge
#176
wolny
closed
9 months ago
9
Add desktop entry on the first start of plantseg after installation
#175
wolny
opened
9 months ago
0
Add foreground/background postprocessing
#174
wolny
opened
9 months ago
2
Support for GUI dataset/channel selection, follow #165
#173
qin-yu
closed
7 months ago
5
PlantSeg latest version, having issue with using CUDA from GUI.
#172
athulrv
closed
9 months ago
4
PyQT is not installed automatically, can't run napari interface
#171
Buglakova
opened
9 months ago
2
Add option to set home_path via PLANTSEG_HOME env-variable.
#170
tibuch
closed
9 months ago
1
Add Zenodo record for generic plant nuclei model
#169
qin-yu
closed
10 months ago
2
Error after updating plantseg
#168
athulrv
closed
9 months ago
12
update plantseg
#167
athulrv
closed
9 months ago
1
Error on the GASP segmentation using GUI: Need more labels than can be represented in the destination type
#166
athulrv
opened
10 months ago
2
Backward compatible `key` & `channel` params for config pipeline
#165
qin-yu
closed
10 months ago
4
could not run GASP clustering on napari ver
#164
tats53
closed
11 months ago
0
Unnecessary check of preprocessing/prediction section configs when only using segmentation function
#163
qin-yu
opened
1 year ago
1
Multichannel network output cannot be specified for segmentation
#162
qin-yu
closed
10 months ago
0
Add training and dataset managemnt
#161
lorenzocerrone
opened
1 year ago
0
Ensure compatibility with models trained with pytorch-3dunet
#160
wolny
closed
1 year ago
1
Add support for training
#159
wolny
closed
7 months ago
2
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