marcnol pyHiM issues - Githubissues

marcnol / pyHiM

Multiplexed DNA-FISH data analysis pipeline

GNU Lesser General Public License v3.0

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issues

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use of 'registered' cellpose image for tracing

#249 marcnol opened 1 week ago
0
changed default use of cli and added comments

#248 marcnol closed 1 week ago
0
Error with image filename

#247 marcnol closed 2 weeks ago
4
use multiple GPUs for segmentation

#246 marcnol opened 2 weeks ago
0
Bug (`trace_filter.py`) - dist_max is an input argument but it's never used

#245 XDevos opened 3 months ago
1
Feature (`trace_filter.py`) - Add possibility to remove different barcodes at the same time

#244 XDevos opened 3 months ago
0
Bug (`deinterleave_channels`) - with raw image from AIRYSCAN

#243 XDevos opened 3 months ago
1
Add a WARNING log file

#242 XDevos opened 4 months ago
0
Deprecated "z-offset" for barcode-mask matching ?

#241 XDevos opened 4 months ago
1
GUI not working > mask_manual.py

#240 olivier469110 opened 4 months ago
0
segmentSources3D does not work without a global alignment dict

#239 marcnol opened 4 months ago
0
pyHiM global alignment crashes

#238 marcnol opened 4 months ago
0
Development

#236 XDevos closed 6 months ago
0
Version 0.9.0

#235 XDevos closed 6 months ago
0
changes left

#234 marcnol closed 6 months ago
0
Tuto cellpose

#233 XDevos closed 7 months ago
0
Update environment yaml

#232 XDevos closed 7 months ago
0
trace_merge.py | Add a label parameter

#231 MarionBardou closed 7 months ago
1
Fix (trqce_filter) - Missing case 'label is None'

#230 XDevos closed 7 months ago
0
Feature (plots_traces) - Highlight unit inside PNG plots

#229 XDevos opened 7 months ago
1
added and modified doc

#228 marcnol closed 7 months ago
0
Feature - Filter masks

#227 XDevos opened 7 months ago
0
Scripts (doc) - Update documentation for post processing scripts

#226 XDevos closed 7 months ago
0
mask_cellpose - apply global shifts

#225 XDevos closed 7 months ago
0
Update environment.yml file for pyHiM installation

#224 XDevos closed 6 months ago
0
Remove outputFile parameter

#223 XDevos opened 7 months ago
0
Convert trace tables to format of Ren Lab

#222 XDevos closed 6 months ago
0
Remove cv2/issue 73

#221 XDevos closed 7 months ago
0
Integrate stardist/196

#220 XDevos closed 7 months ago
0
Feature (DataManager) - Add modern image file formats, such as OME-Zarr

#219 XDevos opened 7 months ago
0
Doc - Tutorial to use cellpose as a replacement for StarDist

#218 XDevos closed 7 months ago
0
Fix (build_traces) - Accept a mask segmentation performed without pyHiM

#217 XDevos closed 7 months ago
0
Update parameters.json model

#216 XDevos closed 7 months ago
0
Doc (parameters.json) - How to personalize filepath inside parameters.json for a home stardist model

#215 XDevos closed 6 months ago
2
Remove extern hard coded path for segmentation models

#214 XDevos closed 7 months ago
0
Doc (localize_3d) - Describe the spot-stitching approach

#213 XDevos closed 6 months ago
4
Doc (README) - Highlight the demo dataset

#212 XDevos closed 6 months ago
0
Interoperability (Segmentation) - pyHiM must integrate Cellpose

#211 XDevos closed 7 months ago
1
Portability (cross-plateform) - pyHiM may run on Linux, macOS and Microsoft Windows

#210 XDevos closed 6 months ago
1
Integrate stardist/196

#209 XDevos closed 7 months ago
0
Feature (Plots) - Allow multiple plotting formats at same time (svg, png, pdf)

#208 XDevos opened 7 months ago
0
Refactor/parameters

#207 XDevos closed 8 months ago
0
datamanager fails to recognize file name in folders

#206 marcnol closed 8 months ago
1
plot_bootstrapping.py error

#205 MarionBardou opened 8 months ago
4
Refactor/folders

#204 XDevos closed 8 months ago
0
nan issue => build_matrix

#203 MarionBardou opened 8 months ago
0
Bug (build_traces) - core dumped when create 3D KDTree

#202 XDevos opened 8 months ago
0
Bug (localize_3d) - error when pyHiM try to segment reference RT image

#201 XDevos opened 8 months ago
0
Bug (mask_2d) - We can't give as input an **unregistered** 2D npy DAPI image

#200 XDevos opened 8 months ago
0
Bug (mask_2d) - The output NPY mask isn't seem to be the stardist output

#199 XDevos closed 6 months ago
1