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gerlichlab
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looptrace
Fork (from EMBL Gitlab) of the looptrace project: https://git.embl.de/grp-ellenberg/looptrace
MIT License
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Consider using `aicsimageio`
#287
vreuter
opened
3 months ago
0
Need to discard data from FOVs with no beads for drift correction in reference timepoint
#285
vreuter
opened
3 months ago
1
Need to write data for nuclear mask layer since pipeline can't handle screenshots
#284
vreuter
closed
1 month ago
2
We should try to remove the upper bound on numpy dependency
#283
vreuter
opened
3 months ago
0
Nuclei segmentation method recommendation is wrong, and pipeline can't parse this value
#282
vreuter
closed
3 months ago
0
We could have a pipeline dependencies group and build (Docker) that doesn't include TensorFlow
#281
vreuter
opened
3 months ago
1
Need better naming for proximity filter strategies, and type refinement
#280
vreuter
closed
2 months ago
1
Dealing with regional spots close together which should be kept and used, but as 1 single ROI
#279
vreuter
opened
3 months ago
5
May need to run `napari` in "headless" mode in pipeline
#278
vreuter
closed
2 months ago
3
Write data for drag-and-drop visualisation of locus-specific spots / points in `napari`
#277
vreuter
closed
3 months ago
0
Could plot counts of instances of each QC fail component reason
#276
vreuter
opened
3 months ago
0
Could normalise heatmaps
#275
vreuter
opened
3 months ago
0
Relax locus grouping requirements
#274
vreuter
closed
4 months ago
0
Requirements for `locusGrouping` should be relaxed and related behavior should be updated accordingly
#273
vreuter
closed
4 months ago
0
Save points for napari
#272
vreuter
closed
4 months ago
0
Spot images files: .zarr should replace .npz
#271
vreuter
closed
1 month ago
1
Should we require every region to specify loci?
#270
vreuter
closed
4 months ago
1
Include annotation and/or coloring based on failed QC reasons (columns available in traces output file)
#269
vreuter
closed
1 month ago
3
_Save_ points overlaying locus-specific spots
#268
vreuter
closed
4 months ago
1
Config redesign 1st step: imaging rounds declaration
#267
vreuter
closed
4 months ago
0
Make `LabelAndFilterRois.buildNeighboringRoisFinder` object-private?
#266
vreuter
closed
2 months ago
1
Need to filter out (QC fail) locus-specific spots when centroid of spot is within 1 standard deviation of any border of the ROI
#265
vreuter
opened
4 months ago
1
Position, time, and channel naming in regional spot visualisation's napari screenshots is 1-based
#264
vreuter
closed
4 months ago
0
Match locus-specific points structure to images structure
#263
vreuter
closed
4 months ago
0
Mostly to locus-specific spot visualisation
#262
vreuter
closed
4 months ago
0
We need to standardise format of header in table-like files for CSV
#261
vreuter
opened
4 months ago
1
Enhancement ideas for regional spot visualisation
#260
vreuter
closed
2 months ago
2
Enhancement ideas for locus-specific spot visualisation
#259
vreuter
closed
2 months ago
4
Create LICENSE
#258
vreuter
closed
4 months ago
0
Create LICENSE
#257
vreuter
closed
4 months ago
1
Candidates to refactor with OME-ZARR / JVM compatibility
#256
vreuter
opened
4 months ago
0
Regional spot visualisation tweaks
#255
vreuter
opened
4 months ago
1
Visualisation of regional spots
#254
vreuter
closed
4 months ago
0
Nuclei refinements
#253
vreuter
closed
4 months ago
0
Add _fine_ drift correction for nuclei
#252
vreuter
opened
5 months ago
0
Some pipeline dependencies could be conditional
#251
vreuter
opened
5 months ago
0
Enforce 1-timepoint-for-nuclei rule
#250
vreuter
opened
5 months ago
1
For Python tests, we should separate dependencies so that lighter tests don't use beefier dependencies of full-pipeline or other integration-like tests
#249
vreuter
closed
5 months ago
0
Use nuclear masks for spot filtration
#248
vreuter
closed
5 months ago
0
Image array indexing needs to be more consistent and robust w.r.t. handling of time, channel, and z dimensions
#247
vreuter
opened
5 months ago
1
We should add tests for `pipeline_precheck` to the Python part of the project
#246
vreuter
opened
5 months ago
0
Generation of nuclei images can result in zarr with incorrect `chunks` and `shape` metadata
#245
vreuter
closed
5 months ago
1
We need better encoding of the nucleus image slicing strategies prior to segmentation
#244
vreuter
opened
5 months ago
0
Allow more than 1 timepoint for nuclei images?
#243
vreuter
closed
5 months ago
2
Combine `Drifter.pos_list` / `Drifter.full_pos_list`
#242
vreuter
opened
5 months ago
0
Reinstating nuclei detection and nuclear masking
#241
vreuter
opened
5 months ago
0
Image folder updates should be per-pipeline-run rather than per-experiment
#240
vreuter
opened
5 months ago
0
Nix shell with pipeline dependencies (`nix-shell --arg pipeline true`) won't work
#239
vreuter
opened
5 months ago
1
Udpate pypiper version to 0.14.0; close #230
#238
vreuter
closed
5 months ago
0
Only consider locus-specific spots from region(s) where they're expected
#237
vreuter
closed
1 month ago
2
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