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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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Allow ability for probe/frame/timepoint grouping to be interpreted as explicit permission rather than prohibition (dually implied implicit permission)
#198
vreuter
closed
8 months ago
0
We should plot number of locus-specific FISH spots per probe/frame/timepoint
#197
vreuter
closed
9 months ago
2
Proximity-based spot filtration: any missing drift should be an error
#196
vreuter
closed
9 months ago
0
Drift correction isn't used in proximity-based filtration of spots
#195
vreuter
closed
9 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
9 months ago
5
Refactor: change DistanceThreshold to an enum
#193
vreuter
opened
9 months ago
0
Spot visualisation
#192
vreuter
closed
5 months ago
1
Bring in `drspot` project
#191
vreuter
closed
8 months ago
0
Add pipeline execution control and restart docs; close #189
#190
vreuter
closed
9 months ago
0
Document the key pipeline restart points, where parameter exploration may be most desirable
#189
vreuter
closed
9 months ago
0
Need tests for spot proximity-based filtration
#188
vreuter
closed
9 months ago
0
Safer image filename parsing, tests, CI
#187
vreuter
closed
9 months ago
0
Need tests for combining imaging folders
#186
vreuter
opened
9 months ago
0
Need tool(s) to count tracing records by (regional, local) spot image timepoint
#185
vreuter
closed
9 months ago
0
.nd2 to dask array / .zarr conversion could be accelerated...
#184
vreuter
opened
9 months ago
0
Deprecated regex escape sequence \d needs updated
#183
vreuter
opened
9 months ago
0
Deprecated pkg_resources.resource_filename call in __init__.py needs updated
#182
vreuter
closed
9 months ago
0
remove noisy messaging
#181
vreuter
closed
9 months ago
0
Finishing tracing and spot extraction fixes
#180
vreuter
closed
9 months ago
0
Tidy up spot bounding and extraction
#179
vreuter
closed
9 months ago
0
Fix spot image bounding for homogeneous accord with ROI image size from config file upon extraction
#178
vreuter
closed
9 months ago
0
Write out reasons to skip certain spot images; align table dimensions for tracing, and fix padding
#177
vreuter
closed
9 months ago
0
fix msg fmt
#176
vreuter
closed
9 months ago
0
guard against negative maximum for slicing image, in any dimension
#175
vreuter
closed
9 months ago
0
More safety, and fixing out-of-bounds spot image boxes
#174
vreuter
closed
9 months ago
0
Feature: absolute minimum number of ROIs for DC, allowing fewer than desired number down to that number
#173
vreuter
closed
8 months ago
1
Spit out maximum number of bead ROIs for shifting to make it pass
#172
vreuter
closed
9 months ago
1
We should plot number of spots detected per regional barcode
#171
vreuter
closed
9 months ago
1
Make JAR's dispensable for Python package
#170
vreuter
closed
9 months ago
0
Make deconvolution input and output keys required in config, make .zarr addition conditional, and make spot proximity filtration conjunctive
#169
vreuter
closed
9 months ago
0
Default proximity filtration is piecewise disjunctive rather than piecewise conjunctive
#168
vreuter
closed
9 months ago
0
Can't use looptrace in REPL when JAR isn't available
#167
vreuter
closed
9 months ago
0
Deconvolution can add a second .zarr extension to position name
#166
vreuter
closed
9 months ago
1
Currently `convert_datasets_to_zarr.py` doesn't reuse code from `image_io.images_to_ome_zarr`
#165
vreuter
opened
9 months ago
0
Parameter inference from .nd2 metadata parsed during conversion to .zarr
#164
vreuter
opened
9 months ago
3
.zarr conversion improvements to make
#163
vreuter
opened
9 months ago
0
ImageHandler.decon_output_path is optional but shouldn't be (via 'decon_output_name optionality in config)
#162
vreuter
closed
9 months ago
0
Make deconvolution earlier and add more config file writing notes
#161
vreuter
closed
9 months ago
0
Make conversion to .zarr and deconvolution play nicely together
#160
vreuter
closed
9 months ago
0
reshape2 is deprecated and should be removed in favor of relying just on data.table
#159
vreuter
closed
9 months ago
0
Use Java 21 while Docker image is still Ubuntu 20 (focal), and require .zarr conversion specification
#158
vreuter
closed
9 months ago
0
Conversion to .zarr isn't parallelised
#157
vreuter
opened
9 months ago
0
Java version should be bumped to 21
#156
vreuter
closed
9 months ago
1
Combining imaging folders and updating dependency versions
#155
vreuter
closed
9 months ago
0
ImageHandler is overly optimistic about uniqueness of (position, timepoint)
#154
vreuter
closed
9 months ago
0
Regional barcode grouping, major padding bugfix, adhoc analysis scripts, and piecewise elimination of array_id, piecewise distance for spots' separation, many tests
#153
vreuter
closed
9 months ago
0
add notes about config file changes and settings suggestions
#152
vreuter
closed
9 months ago
0
Allow writing of drift-corrected images as part of pipeline
#151
vreuter
closed
6 months ago
3
Ensure ROI proximity-based filtration operates only within, not between, each field of view (FOV)
#150
vreuter
closed
9 months ago
0
Adopt kittens to get some typeclass derivation
#149
vreuter
closed
9 months ago
1
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