gerlichlab looptrace issues

gerlichlab / looptrace

Fork (from EMBL Gitlab) of the looptrace project: https://git.embl.de/grp-ellenberg/looptrace

Apache License 2.0

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issues

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Consider producing cross-channel signal analysis in multiple forms

#379 vreuter opened 1 day ago
0
Update documentation for v0.11.0

#378 vreuter opened 1 day ago
0
Different-timepoint merger

#377 vreuter closed 1 day ago
0
Remove regional spot timepoints from big "locus-specific" collection for signal analysis

#376 vreuter opened 2 days ago
0
Better encoding of what's imaged in each channel

#375 vreuter opened 6 days ago
1
Update `NucleusDesignation` and `NucleusNumber` related code such that `0` does _not_ encode non-nuclear, but is illegal

#374 vreuter closed 1 week ago
1
Make distance threshold (proximity filtration, ROI merge) carry units

#373 vreuter opened 1 week ago
1
`roi_id` is wrong, using row index rather than actual ROI index/ID

#372 vreuter closed 1 day ago
0
`roi_number` is useless and confusing

#371 vreuter closed 1 day ago
0
Update spot count plotting/visualisation programs to deal with same- and different-timepoint mergers

#370 vreuter opened 1 week ago
1
Remove local `Eq` and `Order` instances for `FieldOfViewLike`

#369 vreuter opened 1 week ago
0
Non-pairwise-proximal ROIs which should be grouped could be combined to separate merge results

#368 vreuter closed 1 day ago
1
Start being more precise about units of measure

#367 vreuter closed 2 weeks ago
0
Migrate pixel quantity to `gerlib`

#366 vreuter opened 2 weeks ago
0
Migrate `CellEncoder[EuclideanDistance]` to `gerlib`

#365 vreuter opened 2 weeks ago
0
Representing processing state of data on disk

#364 vreuter opened 2 weeks ago
0
Representing units in on-disk representation of numeric values

#363 vreuter opened 2 weeks ago
1
For the region spot pairwise distances, `inputIndex1` and `inputIndex2` should just use the ROI IDs instead

#362 vreuter closed 1 day ago
0
To avoid confusion, `inputIndex1` and `inputIndex2` in the locus spot pairwise distances output file should be something like `recordNumber`

#361 vreuter closed 2 weeks ago
1
Distance rendering in locus-specific pairwise distances file shows EuclideanDistance wrapper

#360 vreuter closed 2 weeks ago
0
Regional pairwise distances appear to be in pixels, not nanometers

#359 vreuter closed 2 weeks ago
0
Regional spot coordinate fixes

#358 vreuter closed 2 weeks ago
0
Replace `R` with `xchart`

#357 vreuter opened 3 weeks ago
0
Spot coordinates are drift corrected too early (during proximity-based filtration)

#356 vreuter closed 2 weeks ago
1
Coordinates of final stage regional spots are wrong

#355 vreuter closed 2 weeks ago
3
Rename `index` to `roiId` (or similar)

#354 vreuter opened 3 weeks ago
0
Center of merge result doesn't appear correct

#353 vreuter closed 1 month ago
2
Regional spots aren't drift corrected for visualisation

#352 vreuter closed 1 month ago
2
Version 0.10 release prep

#351 vreuter closed 3 weeks ago
1
Merge ROIs from the same timepoint which are close together

#350 vreuter closed 1 month ago
0
Try to remove indirect / derived need for UCAR resolver in `build.sbt`

#349 vreuter opened 4 months ago
0
v0.9.1 version bump, fixing use of method like property

#348 vreuter closed 4 months ago
0
Use TensorFlow base image for Docker, allowing bump up to Python 3.11

#347 vreuter closed 4 months ago
0
Preserve FOV naming for nuclear mask centroid table files for visualisation

#346 vreuter closed 4 months ago
0
Preserve correct FOV-based names for nuclear masks when a field of view is removed

#345 vreuter closed 4 months ago
0
Nuclear mask makes are incorrect when a field of view is removed, bad visualisation

#344 vreuter closed 4 months ago
0
Apply fine drift correction for nuclei image(s) and use it in ROI-to-nucleus assignment

#343 vreuter opened 4 months ago
2
Read spot detection / regional imaging timepoints only from imaging rounds config file, not params config file

#342 vreuter closed 4 months ago
0
Use `gerlib`, v0.6.0

#341 vreuter closed 4 months ago
0
Replace `scala-csv` with `fs2-data`

#340 vreuter opened 4 months ago
2
Consider tests with `Nonnegative` values having `Double.PositiveInfinity`

#339 vreuter opened 4 months ago
0
Prohibit `spot_frame` in parameters config

#338 vreuter closed 4 months ago
0
Addition of analysis of non-FISH signal in regions defined by FISH signal

#337 vreuter opened 5 months ago
12
Consider `cats-scalacheck` dependency to replace maually crafted instances

#336 vreuter closed 5 months ago
1
Add documentation of resource use hooks for coarse drift correction

#335 vreuter opened 5 months ago
0
Tasks for switching to per-FOV structure, cluster-deployed execution

#334 vreuter opened 5 months ago
0
alleviate some resource pressure during coarse drift correction

#333 vreuter closed 5 months ago
0
Coarse drift correction hits memory / resource errors sometimes

#332 vreuter closed 5 months ago
0
Bugfix for Issue 330, `lstrip` --> `removeprefix`

#331 vreuter closed 5 months ago
0
`str.lstrip` where `str.removeprefix` belongs can result in `KeyError` when accessing table(s)

#330 vreuter closed 5 months ago
0