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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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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
Update R, fix regional spot counts visualisation invocation
#236
vreuter
closed
5 months ago
0
Try to remove deconvolution
#235
vreuter
opened
5 months ago
2
Feature: ability to compute distances between locus-specific spots from different trace IDs
#234
vreuter
closed
3 months ago
2
Regional spot count charts are incorrectly produced indirectly by pipeline even though correctly produced directly by R script
#233
vreuter
closed
5 months ago
2
Tolerate pairwise distance input so long as needed fields are present
#232
vreuter
closed
5 months ago
0
Regional barcode distance program needs to relax header assumption
#231
vreuter
closed
5 months ago
0
Try upgrading pypiper
#230
vreuter
closed
5 months ago
1
TODO: test that any failure to extract small spot image for tracing generates expected error, and that results in blackout frame (all zeroes)
#229
vreuter
opened
5 months ago
0
We need to explicitly, concretely specify proximity-based spot filtration behavior for spots from the same regional barcode
#228
vreuter
closed
2 months ago
1
Ignore/skip image stacks with too few bead ROIs for drift correction
#227
vreuter
closed
5 months ago
0
Downsampling could (should?) first take averages of pixels
#226
vreuter
opened
5 months ago
0
JSON file for reasons for skipping spot image extraction isn't well formatted
#225
vreuter
closed
5 months ago
0
Off-centering of signal in spot images for tracing, even in regional barcode timepoints
#224
vreuter
closed
5 months ago
1
As currently reported, coarse drifts in `*_dc_rois.csv` file are RELATIVE (to the regional spot frame) rather than to DC reference frame
#223
vreuter
opened
5 months ago
2
Skip data for points with too few ROIs fror drift correction
#222
vreuter
closed
5 months ago
0
Consider making a single bead ROIs file per FOV
#221
vreuter
opened
5 months ago
0
Once conversion to .zarr is done, we could check time dimension's match to `frame_name` in config
#220
vreuter
opened
5 months ago
4
Pass nothing for the `images_folder` for the `ImageHandler` creation for bead ROI generation
#219
vreuter
opened
5 months ago
1
Support _permissive_ (rather than _prohibitive_) regional barcode timepoint grouping
#218
vreuter
closed
5 months ago
0
add regional pairwise distances to pipeline; #199
#217
vreuter
closed
5 months ago
0
Centralise and promulgate distinction b/w regional and locus-specific barcode imaging timepoints
#216
vreuter
closed
5 months ago
0
Rethinking config section for declaring probe names
#215
vreuter
closed
4 months ago
1
Config section for which locus timepoints group with which regional timepoints
#214
vreuter
closed
2 months ago
1
Retyping GroupName as RegionId
#213
vreuter
closed
5 months ago
0
Rename FrameIndex as Timepoint
#212
vreuter
closed
5 months ago
0
Retype grouping element for simple distance computation from `GroupName` (String) to `RegionId` (Timepoint)
#211
vreuter
closed
5 months ago
0
Rename `FrameIndex` as `Timepoint`
#210
vreuter
closed
5 months ago
0
Add JSON representation of regional barcode spots / ROIs
#209
vreuter
opened
5 months ago
0
Adopt logging in JVM part of project
#208
vreuter
closed
2 months ago
3
New release automation
#207
vreuter
opened
5 months ago
0
Minimal and maximal config examples
#206
vreuter
opened
5 months ago
0
Add pairwise distance computation to pipeline, and more directly call JVM programs
#205
vreuter
closed
5 months ago
0
We need documentation of the outputs and their structure
#204
vreuter
closed
2 months ago
0
Drift correction robustness, docs update,
#203
vreuter
closed
5 months ago
0
Replace timepoint index with probe name in plots of spot counts
#202
vreuter
closed
5 months ago
1
We should test that the pipeline execution control / restart doc is current
#201
vreuter
opened
5 months ago
0
Ideas: measuring linearity of DNA
#200
vreuter
opened
5 months ago
0
We should be able to compute distances between regional spot centroids, too
#199
vreuter
closed
5 months ago
1
Allow ability for probe/frame/timepoint grouping to be interpreted as explicit permission rather than prohibition (dually implied implicit permission)
#198
vreuter
closed
5 months ago
0
We should plot number of locus-specific FISH spots per probe/frame/timepoint
#197
vreuter
closed
5 months ago
2
Proximity-based spot filtration: any missing drift should be an error
#196
vreuter
closed
6 months ago
0
Drift correction isn't used in proximity-based filtration of spots
#195
vreuter
closed
6 months ago
0
Test: ensure that `phase_cross_correlation` ('cc') and Gaussian fit ('fit') methods give same drift correction direction and accord with usage later in processing
#194
vreuter
opened
6 months ago
5
Refactor: change DistanceThreshold to an enum
#193
vreuter
opened
6 months ago
0
Spot visualisation
#192
vreuter
closed
2 months ago
1
Bring in `drspot` project
#191
vreuter
closed
5 months ago
0
Add pipeline execution control and restart docs; close #189
#190
vreuter
closed
6 months ago
0
Document the key pipeline restart points, where parameter exploration may be most desirable
#189
vreuter
closed
6 months ago
0
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