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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
89
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30
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Some tests for Zarr are invalid
#234
qin-yu
closed
2 months ago
0
Fix `CYX`/`CZYX` pad/halo, fix `io.zarr`/tests, fix typing, refactor model load
#233
qin-yu
closed
2 months ago
0
Mirror pad (and halo?) doesn't consider 4D (`CZYX`) cases
#232
qin-yu
closed
2 months ago
0
Type Fix: `np.array` is not a type, change to `np.ndarray`
#231
qin-yu
closed
2 months ago
1
Documentation: Migrate to MkDocs; update installation, README, and logo
#230
qin-yu
closed
2 months ago
1
Dev Env: Add BioImage.IO Core dependency and fix CUDA installation
#229
qin-yu
closed
2 months ago
0
Broken Environment - RuntimeError: GET was unable to find an engine to execute this computation
#228
qin-yu
closed
2 months ago
4
Napari GUI: Fix voxel size precision, font size, and rearrange widgets
#227
qin-yu
closed
2 months ago
0
Napari UI: Add model widget only takes two decimal in resolution
#226
qin-yu
closed
2 months ago
1
Need to make use of predictions from multiple models
#225
qin-yu
opened
2 months ago
0
Re-train all PlantSeg models to eliminate hallucination during inference
#224
qin-yu
opened
3 months ago
0
Fix Tiling Artefact: intensity normalisation was correct
#223
qin-yu
closed
3 months ago
0
PlantSeg pipelines do not reuse code
#222
qin-yu
opened
3 months ago
1
add widget manager for extra-pred and extra-seg
#221
lorenzocerrone
closed
3 months ago
1
Fix halo implementation and tiling artefact
#220
qin-yu
closed
3 months ago
5
Conda build workflow fails because of branch name has `/` or `-`
#219
qin-yu
closed
3 months ago
3
Too many elements in extra-seg
#218
lorenzocerrone
closed
3 months ago
3
"Run Image Rescaling" widget throw errors when no image is opened
#217
qin-yu
closed
1 month ago
1
Central model records
#216
qin-yu
closed
3 months ago
2
Models and their attributes are loaded on demand without centered control
#215
qin-yu
closed
3 months ago
1
Out of (host) memory at Data Pre-Processing step
#214
bobonannan
opened
4 months ago
3
Napari UI: Widgets too wide yet don't have enough space for numbers to show
#213
qin-yu
closed
2 months ago
6
extend channel selection
#212
lorenzocerrone
closed
4 months ago
3
Add validation, adaptation and halo to prediction widgets
#211
qin-yu
closed
4 months ago
1
Allow direct search and download from BioImage Model Zoo
#210
qin-yu
opened
4 months ago
7
Napari GUI: Parameter/config checking happens at widget runtime
#209
qin-yu
opened
4 months ago
2
`statics_kwargs` vs `runtime_kwargs`
#208
qin-yu
opened
4 months ago
2
Add option to only run official models in "Try all Available Models"
#207
qin-yu
closed
4 months ago
0
`cudnn` needs to be installed for some systems
#206
qin-yu
closed
4 months ago
0
`patch_halo` seems to be ignored
#205
qin-yu
closed
4 months ago
6
No channel selection in "Open File" widget
#204
qin-yu
closed
4 months ago
2
No voxel size information on images saved from PlantSeg Napari GUI
#203
qin-yu
closed
4 months ago
1
Add widget: remove objects using a probability map
#202
qin-yu
closed
4 months ago
6
v1.6.5 crash on launch
#201
qin-yu
closed
5 months ago
0
It would be nice to know exactly which instances are removed by postprocessing steps
#200
qin-yu
opened
5 months ago
0
Napari UI: Coordinate doesn't reflect real position
#199
qin-yu
opened
5 months ago
0
Napari UI: Renamed layers no updated in dropdown lists
#198
qin-yu
opened
5 months ago
2
Need to change link to docs on conda-forge
#197
qin-yu
closed
5 months ago
0
Linux and Windows installation commands differ
#196
qin-yu
closed
5 months ago
2
No orthoviewer
#195
qin-yu
opened
5 months ago
1
Transfer PlantSeg from HCI to Kreshuk Lab
#194
qin-yu
closed
2 months ago
5
Rename generic plant nuclear model for paper submission
#193
qin-yu
closed
5 months ago
2
Generic plant nuclei model should be found as `PlantSeg_3Dnuc_platinum`
#192
qin-yu
closed
5 months ago
0
Redirect all Wiki links to new doc and improve READMEs
#191
qin-yu
closed
5 months ago
1
Strong tiling artifacts
#190
Buglakova
closed
3 months ago
3
Help to choose the correct scale to apply the network
#189
Buglakova
opened
5 months ago
2
No instructions for how to do proofreading
#188
Buglakova
closed
5 months ago
1
Links in Docs and README still point to Wiki
#187
qin-yu
closed
5 months ago
2
Erosion option for nuclei channel in Lifted MultiCut and Segmentation Fix in Extra-Seg
#186
qin-yu
opened
5 months ago
0
Only PlantSeg v1.6.0 available on conda-forge
#185
qin-yu
closed
5 months ago
5
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