Note: This is not backwards compatible with previous run-throughs of OMP. You must delete the OMP notebook page and re-run.
Changes
OMP spots are now found as the score local maxima instead of the coefficient local maxima (#271).
The OMP mean spot is more accurate by increasing the config default shape_coefficient_threshold from 0.01 -> 0.4 (same value as high_coef_bias).
OMP getting spot colours is now faster and more robust to the RAM available.
OMP is now faster. On a 73 gene panel with 7 sequencing channels, the fastest time is 25 minutes per tile. I think about an extra 5 minutes per tile can be saved through gene batching (#274) but this is not a priority.
Slightly better OMP unit testing.
Detect spots removing duplicate local maxima is now more robust.
New detect spots unit test.
Checklist
[x] I have updated the changelog.txt, if applicable.
[x] I have bumped the software version in _version.py, if applicable.
[x] I have checked that the unit tests passed.
[x] I have checked that Minnie and/or RoboMinnie passed.
Note: This is not backwards compatible with previous run-throughs of OMP. You must delete the OMP notebook page and re-run.
Changes
shape_coefficient_thresholdfrom0.01->0.4(same value ashigh_coef_bias).Checklist
changelog.txt, if applicable._version.py, if applicable.