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Issues list

Allow False for value of key for filtration of FISH spots by bead proximity, or allow it to be missing configuration enhancement New feature or request
#440 opened Mar 19, 2025 by vreuter v0.15
The filtered bead counts heatmap (by (FOV, time) pair) is broken bug Something isn't working likely solved
#437 opened Feb 28, 2025 by vreuter v0.14
@vreuter
beadIndex column occurs twice in the each bead ROIs CSV bug Something isn't working likely solved
#436 opened Feb 28, 2025 by vreuter v0.14
@vreuter
Merges are not iterative question Further information is requested
#435 opened Feb 27, 2025 by vreuter v0.15
@vreuter @TLSteinacker
1
Rethinking the "fine" (subpixel resolution) drift correction brainstorming enhancement New feature or request pipeline question Further information is requested
#434 opened Feb 26, 2025 by vreuter
@vreuter @TLSteinacker
1
We could generate fiducial bead ROIs only for the reference timepoint efficiency pipeline priority high
#433 opened Feb 26, 2025 by vreuter v0.14
@vreuter
We should use physical length units for the distance threshold for spot merger enhancement New feature or request priority high refactor
#432 opened Feb 22, 2025 by vreuter v0.14
@vreuter
Data stacking for locus spots visualisation is broken as of v0.12.0, for the case of things other than merged ROIs for trace groups bug Something isn't working priority high
#431 opened Feb 22, 2025 by vreuter v0.14
@vreuter
Remove soon-to-be-extra check for negative z-coordinate refactor
#427 opened Feb 19, 2025 by vreuter v0.15
@vreuter
Add nucleus designation/attribution column to the later-stage output files enhancement New feature or request pipeline
#421 opened Jan 27, 2025 by vreuter v0.15
@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 v0.14
Regional spots' pairwise distances program can lead to OutOfMemory error pipeline
#416 opened Jan 18, 2025 by vreuter v0.15
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 v0.15
@vreuter
ImageHandler aggression: parsing contents of analysis subfolder pipeline umbrella
#411 opened Jan 17, 2025 by vreuter
1 of 2 tasks
@vreuter
Consider / Confirm: require locusGrouping section if doing ROI merge for tracing (mergeRulesForTracing section) configuration priority high
#409 opened Jan 10, 2025 by vreuter v0.14
@vreuter
Omit voxel for regional timepoint from locus spot visualization stack
#408 opened Jan 3, 2025 by vreuter v0.15
@vreuter
1
Deprecate empirical point-spread function (PSF) determination configuration documentation Improvements or additions to documentation
#405 opened Dec 19, 2024 by vreuter
3 tasks
v0.15
@vreuter
Visualisation of tracing structures enhancement New feature or request visualisation
#404 opened Dec 7, 2024 by vreuter v0.15
@vreuter
Switching to TetraSpeck beads likely solved umbrella
#403 opened Dec 6, 2024 by vreuter
1 of 3 tasks
v0.14
@vreuter
Apply proximity filter between beads and FISH spots enhancement New feature or request likely solved
#401 opened Dec 6, 2024 by vreuter v0.14
@vreuter
Restructuring data-driven tests for better encapsulation and less fragility good first issue Good for newcomers help wanted Extra attention is needed testing
#394 opened Dec 1, 2024 by vreuter
We could add a parameter for the minimum number of trace ID merge group members configuration enhancement New feature or request refactor
#389 opened Nov 28, 2024 by vreuter
2 tasks
v0.15
We could make trace ID merge behavior configurable on a per-group basis configuration enhancement New feature or request refactor
#387 opened Nov 28, 2024 by vreuter v0.15
We could add a parameter for the maximum number of trace ID merge group members brainstorming configuration enhancement New feature or request
#386 opened Nov 28, 2024 by vreuter v0.15
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