Updated ome-types

Updated ome-types inside the container to account for the latest XML metadata standards.

s3seg-large file compression

Merge pull request #23 from Yu-AnChen/master

Compress output image files

Additional RGB image reading

Fix reading channels from RGB image (probability map)

Channel reading from RGB images

Fix reading channels from RGB image (probability map)

maxima-h to float

Merge pull request #20 from Yu-AnChen/patch-6

Fix bug - set `--maxima-h` typing to float

update file path for qc files for s3seg-large

Merge pull request #17 from Yu-AnChen/patch-4

Fix QC file location in large branch

Add pixel size parsing and write segmentation QC file

• Parse pixel size metadata, which can be overwritten by manual input, and write it to the output ome-tiff
• Write QC files, currently 3+ channels - mask outer outline, contour probability map, and intensity rescaled channel image(s) based on the --probMapChan parameter
• Update dependencies (in dockerfile)

An implementation variation to handle large-scale images

An additional implementation variant is available in the large/ subfolder. The corresponding container is available as labsyspharm/s3segmenter:1.4.0-large. The default command-line interface matches the standard implementation.

save spot mask file

1.3.18

minor changes

install imagecodecs

1.3.17

Update Dockerfile