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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
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`str.lstrip` where `str.removeprefix` belongs can result in `KeyError` when accessing table(s)
#330
vreuter
closed
5 months ago
0
Ensure drift correction is applied for regional spot pairwise distance computation
#329
vreuter
closed
2 weeks ago
2
Ensure separation of regional timepoint spot fits from locus timepoint spot fits
#328
vreuter
closed
2 weeks ago
2
Apply flat-field correction
#327
vreuter
opened
6 months ago
0
Smooth background for subtraction in tracing
#326
vreuter
opened
6 months ago
1
Casting from `np.uint16` to `np.int16` when subtracting background during tracing
#325
vreuter
closed
6 months ago
0
Store background-subtracted data in the locus spots visualisation
#324
vreuter
closed
6 months ago
0
With new use of `locusGrouping`, first timepoint in group is zeroed-out by background subtraction
#323
vreuter
closed
6 months ago
0
Separate extraction of background data
#322
vreuter
closed
6 months ago
1
We need more stable, sustainable conversion of ND2 to ZARR
#321
vreuter
opened
6 months ago
1
Ensure that only locus time timepoints for which spots volumes will actually be extracted have their data ever read off disk.
#320
vreuter
closed
6 months ago
2
Release 0.5.0
#319
vreuter
closed
6 months ago
0
Bead count (unfiltered or filtered) can be NA
#318
vreuter
closed
6 months ago
0
Write out metadata from the `nd2` files
#317
vreuter
opened
6 months ago
1
Make coarse drift correction incremental like fine drift correction
#316
vreuter
opened
6 months ago
1
We should raise an error if the minimum separation threshold for regional spots is too big
#315
vreuter
opened
6 months ago
0
Add examples of each type of proximity-based filtration section of imaging rounds config
#314
vreuter
closed
6 months ago
0
Should add step to set up visualisation of nuclei / nuclear masks
#313
vreuter
closed
6 months ago
0
Nuclear masks could be compressed
#312
vreuter
closed
6 months ago
0
Need to add step to write data which will be well structured for regional spot visualisation
#311
vreuter
closed
6 months ago
0
Document more thoroughly the `proximityFilterStrategy` section and its implications
#310
vreuter
closed
6 months ago
0
Make the requirement for `minimumPixelLikeSeparation` appropriately conditional on `semantic` of `proximityFilterStrategy`
#309
vreuter
closed
7 months ago
0
With `UniversalProximityPermission`, `minimumPixelLikeSeparation` is incorrectly required
#308
vreuter
closed
7 months ago
1
We should dynamically version the project
#307
vreuter
opened
7 months ago
0
Better proximity filter type naming and refinement
#306
vreuter
closed
7 months ago
0
Use spot detection from `spotfishing`
#305
vreuter
closed
7 months ago
0
Allow a locus-specific timepoint to _not_ be in a value of a member of `locusGrouping` if it's in `tracingExclusions`
#304
vreuter
closed
6 months ago
2
Simplify the construction of Tracer so it's not reading so many things eagerly
#303
vreuter
closed
6 months ago
0
Move nuclear mask data write to as soon as it's available in pipeline processing
#302
vreuter
closed
6 months ago
0
Consider providing deconvolution on JVM
#301
vreuter
opened
8 months ago
1
Pairwise distances b/w regional spots should be computed for all filtrations (or not)
#300
vreuter
opened
8 months ago
0
Add StarDist as nuclei segmentation method
#299
vreuter
opened
8 months ago
0
Support user specification of nuclear masks
#298
vreuter
opened
8 months ago
0
Ancillary visualisations possbily meriting plugin development
#297
vreuter
closed
7 months ago
2
Regional spot count plotting is attempted before filtering spots for nuclei inclusion
#296
vreuter
closed
8 months ago
1
Add key-value boolean hook to loosen validation of locus-to-region mapping
#295
vreuter
closed
6 months ago
0
Add precheck that validates rounds config
#294
vreuter
closed
6 months ago
0
Update filename (maybe) and wording of control flow / restart doc
#293
vreuter
closed
6 months ago
1
Try to add email status for pipeline
#292
vreuter
opened
8 months ago
0
Consider adding `--skips` to skip pipeline step(s)
#291
vreuter
closed
6 months ago
0
Should update dependencies, Scala to 3.4.0
#290
vreuter
closed
7 months ago
0
Folder combination program is too sensitive to filenames with commas and spaces
#289
vreuter
closed
8 months ago
3
Auxiliary tool for using drift correction to write shifted images
#288
vreuter
opened
8 months ago
6
Consider using `aicsimageio`
#287
vreuter
opened
8 months ago
0
Need to discard data from FOVs with no beads for drift correction in reference timepoint
#285
vreuter
closed
1 month ago
4
Need to write data for nuclear mask layer since pipeline can't handle screenshots
#284
vreuter
closed
6 months ago
2
We should try to remove the upper bound on numpy dependency
#283
vreuter
opened
8 months ago
0
Nuclei segmentation method recommendation is wrong, and pipeline can't parse this value
#282
vreuter
closed
8 months ago
0
We could have a pipeline dependencies group and build (Docker) that doesn't include TensorFlow
#281
vreuter
opened
8 months ago
1
Need better naming for proximity filter strategies, and type refinement
#280
vreuter
closed
7 months ago
1
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