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166 Open 185 Closed
166 Open 185 Closed
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Issues list

We could use a more modern version of nd2 likely solved refactor
#423 opened Jan 28, 2025 by vreuter
1 task
v0.14
Single-channel tracing crashes pipeline enhancement New feature or request
#422 opened Jan 27, 2025 by vreuter v0.12
@vreuter
1
Add nucleus designation/attribution column to the later-stage output files enhancement New feature or request pipeline
#421 opened Jan 27, 2025 by vreuter v0.14
@vreuter
Iteration over subpixel localization arguments yields incorrect timepoints, in general, when using locus grouping blocking bug Something isn't working configuration likely solved priority high
#420 opened Jan 23, 2025 by vreuter v0.12
@vreuter
Visualisations for various record counts by trace group brainstorming question Further information is requested visualisation
#419 opened Jan 22, 2025 by vreuter
@vreuter @TLSteinacker
2
Consider changes to regional spots' pairwise distances program
#417 opened Jan 18, 2025 by vreuter v0.13
Regional spots' pairwise distances program can lead to OutOfMemory error pipeline
#416 opened Jan 18, 2025 by vreuter v0.13
Turning off spot filtration by nuclei (Setting spot_in_nuc to False) breaks spot counts visualisation configuration pipeline
#415 opened Jan 17, 2025 by vreuter v0.13
@vreuter
Table parse crashes when file (data frame) is empty bug Something isn't working likely solved pipeline
#414 opened Jan 17, 2025 by vreuter v0.12
@vreuter
Forgetting pixelSeparationBeneathWhichSpotRoisWillMerge key in the parameters configuration file fails to be caught in pipeline precheck bug Something isn't working configuration likely solved pipeline
#413 opened Jan 17, 2025 by vreuter v0.12
@vreuter
Failure to parse, during ImageHandler intialization`, any content of analysis subfolder results in logging warning likely solved
#412 opened Jan 17, 2025 by vreuter v0.12
@vreuter
ImageHandler aggression: parsing contents of analysis subfolder pipeline umbrella
#411 opened Jan 17, 2025 by vreuter
1 of 2 tasks
@vreuter
reg_ref_frame use isn't caught by pipeline_precheck bug Something isn't working configuration likely solved
#410 opened Jan 17, 2025 by vreuter v0.12
@vreuter
Consider / Confirm: require locusGrouping section if doing ROI merge for tracing (mergeRulesForTracing section) configuration
#409 opened Jan 10, 2025 by vreuter v0.13
@vreuter
Omit voxel for regional timepoint from locus spot visualization stack
#408 opened Jan 3, 2025 by vreuter v0.12.1
@vreuter
1
Track/store reindexed trace ID (for each FOV or (FOV, trace group) value) enhancement New feature or request visualisation
#407 opened Dec 19, 2024 by vreuter v0.12.1
@vreuter
Track/store the reindexed (0-based) locus timepoints (per FOV or (FOV, trace group) combination) enhancement New feature or request visualisation
#406 opened Dec 19, 2024 by vreuter
1 task
v0.12.1
@vreuter
Deprecate empirical point-spread function (PSF) determination configuration documentation Improvements or additions to documentation
#405 opened Dec 19, 2024 by vreuter
3 tasks
v0.13
@vreuter
Visualisation of tracing structures enhancement New feature or request visualisation
#404 opened Dec 7, 2024 by vreuter v0.13
@vreuter
Switching to TetraSpeck beads umbrella
#403 opened Dec 6, 2024 by vreuter
2 tasks
v0.13
@vreuter
Changes to locus spot visualisation enhancement New feature or request umbrella visualisation
#402 opened Dec 6, 2024 by vreuter
1 of 4 tasks
v0.12.1
@vreuter
Apply proximity filter between beads and FISH spots enhancement New feature or request
#401 opened Dec 6, 2024 by vreuter v0.13
@vreuter
Mask out TetraSpeck beads with nucler regions enhancement New feature or request
#400 opened Dec 6, 2024 by vreuter v0.13
@vreuter
Prioritise trace group/structure name and locus timepoints for sorting records in locus pairwise distances enhancement New feature or request likely solved
#396 opened Dec 2, 2024 by vreuter
2 tasks done
v0.12
@vreuter
Test that no duplication of records is done in locus pairwise distances likely solved testing
#395 opened Dec 2, 2024 by vreuter v0.12
@vreuter
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