Merge segmentations results from different runs, e.g. FOV
into a single segmetation file. This is done by combining cells if the intersection over union
is bigger than a set threshold.
This approach is similar to the stichting that is done in cellpose.
Usage: merge-baysor [OPTIONS] [FILES]...
Arguments:
[FILES]... The Baysor output files.
These files must include the following columns:
- transcript_id
- cell
Options:
--threshold <THRESHOLD>
Threshold for stitching. If the IOU for two cells is greater that the
threshold, they will be merged [default: 0.2]
--additional-columns <ADDITIONAL_COLUMNS>
Additional columns that will be included in the final output CSV file
[default: x y z qv overlaps_nucleus gene]
--outfile <OUTFILE>
Output file [default: out.csv]
-h, --help
Print help
-V, --version
Print version
