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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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Ensure proximity-based spot filtration removes ALL proximal spots (not just the first one or a subset)
#148
vreuter
closed
9 months ago
1
Ensure that minimum spot separation applies to ALL regional barcodes (rather than to none) if no groupings are specified
#147
vreuter
closed
9 months ago
0
Ensure that minimum spot separation is treated component-wise, not Euclidean
#146
vreuter
closed
9 months ago
1
Single FISH spot (locus-specific) frames/timepoints aren't distinguished from regional ones at the type level
#145
vreuter
closed
8 months ago
2
Refinement type: distance
#144
vreuter
opened
10 months ago
0
Does minimum spot distance separation work in real space or downsampled?
#143
vreuter
closed
9 months ago
1
Centralise overwrite parameterisation
#142
vreuter
opened
10 months ago
0
Ensure program behavior in case every timepoint is skipped for spot extraction for an ROI
#141
vreuter
opened
10 months ago
0
Pad spot images for tracing only in z, not in x or y -- EXCEPT: background frame
#140
vreuter
opened
10 months ago
2
Consider padding with 'linear_ramp' rather than 'edge' values
#139
vreuter
closed
9 months ago
3
Accommodate multi-channel signal extraction
#138
vreuter
opened
10 months ago
0
Accommodate file naming structure/scheme in which timepoints are repeated (RNA)
#137
vreuter
closed
9 months ago
2
Padding is all-zeros everywhere in *_dc_rois.csv file
#136
vreuter
opened
10 months ago
2
With padding, all bounding box sizes should be equal (at least when using `roi_image_size`)
#135
vreuter
opened
10 months ago
0
For each ROI, trace spot image from that ROI's detection timepoint should be brighter (in one or more senses, TBD) than the trace spot image for that ROI from all other timepoints
#134
vreuter
opened
10 months ago
0
Mismatch on shape among trace spot images from same ROI causes all zeros
#133
vreuter
opened
10 months ago
4
Why are reference frames' coarse drift values subtracted from other frame's coarse drift values for spot extraction?
#132
vreuter
opened
10 months ago
0
Why are coarse drifts subtracted, and fine drifts are added?
#131
vreuter
opened
10 months ago
1
Where and how is coarse drift correction used?
#130
vreuter
closed
10 months ago
2
Drift correction file should contain number of records equal to product of number of fields of view and number of hybridisation rounds (timepoints).
#129
vreuter
opened
10 months ago
0
The tuple (FOV, refFrame, time, ROI ID) should unique identify any row in the regional barcodes (initial) ROI file
#128
vreuter
opened
10 months ago
0
Consider parsing .zarr metadata and files themselves with a Java/Scala library
#127
vreuter
opened
10 months ago
1
Pixel-to-nanometer conversion is derivable from .zarr metadata, no need to specify in config file
#126
vreuter
opened
10 months ago
1
Distinguishing between spot detection methods
#125
vreuter
opened
10 months ago
0
Push more spot detection parameters into config
#124
vreuter
opened
10 months ago
0
Improvements made during bead / drift optimisation
#123
vreuter
closed
10 months ago
0
Regional spot ID is lost when building traces; preserve it
#122
vreuter
opened
10 months ago
2
"coarse" is spelled as "course" in many places
#121
vreuter
closed
10 months ago
0
We no longer need the per-frame boxplot chart of detected bead counts
#120
vreuter
closed
10 months ago
0
Decide about which post-tracing QC analyses and visualisations to run automatically
#119
vreuter
closed
5 months ago
0
Why is metadata from only the last folder processed used for zarr creation
#118
vreuter
opened
10 months ago
0
Ensure JAR isn't duplicated in Docker image
#117
vreuter
opened
10 months ago
0
Test for proper warnings saving when (pos, frame) pair(s) lack enough ROIs for drift correction accuracy
#116
vreuter
closed
10 months ago
0
Explain QC pass / fail reasons
#115
vreuter
opened
10 months ago
1
Dynamic definition of filters for spot centroid coordinates
#114
vreuter
closed
10 months ago
0
Clipping after background subtraction
#113
vreuter
opened
10 months ago
0
Nonstandard regions around spots
#112
vreuter
closed
10 months ago
3
Bead ROI count detection visualisation
#111
vreuter
closed
10 months ago
2
Dynamic definition of maximal distance between single probe and regional spot center
#110
vreuter
closed
10 months ago
1
We need automatic tests
#109
vreuter
closed
9 months ago
0
Do not reuse beads / bead ROIs from actual drift correction for drift correction accuracy analysis
#108
vreuter
closed
10 months ago
2
Filter beads for minimum separation distance
#107
vreuter
opened
11 months ago
0
Spot preview: beads and FISH spots
#106
vreuter
closed
8 months ago
1
New drift correction code results in nonzero fine drift for reference points
#105
vreuter
opened
11 months ago
0
Use CSV reading wrapper to fix the fact that we typically have index_col=0
#104
vreuter
closed
8 months ago
0
Drift correction should always have all 0 values for the coordinate shifts for rows where the timepoint/frame is the reference one from the config file (for all fields of view).
#103
vreuter
opened
11 months ago
1
Look for fit sharing possibilities in drift correction accuracy analysis
#102
vreuter
closed
11 months ago
2
Drift correction and DC accuracy analysis should share detected bead ROIs
#101
vreuter
closed
10 months ago
0
Drift-corrected bead ROI images could be saved in drift correction accuracy analysis
#100
vreuter
closed
11 months ago
1
Drift correction accuracy file should have 0 drift error at reference point, regardless of that point
#99
vreuter
closed
11 months ago
1
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