spacetx-biohub-writer

Conversion tool from biohub's DB format to spacetx format

Required columns in the CSV

Column	Description
fov	Field of View identifier. Should be an integer.
round	Round label. Should be an integer.
ch	Channel label. Should be an integer.
zplane	Zplane label. Should be an integer.
xc_min	Minimum physical x-coordinate for the tile
xc_max	Maximum physical x-coordinate for the tile
yc_min	Minimum physical y-coordinate for the tile
yc_max	Maximum physical y-coordinate for the tile
zc_min	Minimum physical z-coordinate for the tile
zc_max	Maximum physical z-coordinate for the tile
path	Relative path to the tile, as specified from the s3_prefix argument
sha256	SHA256 checksum of the tile

Example

Converting from a single CSV representing an image in an experiment.

% spacetx_biohub_writer --csv-file primary primary.csv --s3-prefix  s3://starfish.data.spacetx/osmFISH/formatted/20190626/ --tile-width 2048 --tile-height 2048 -o output

Converting from multiple CSVs representing an image in an experiment.

% spacetx_biohub_writer --csv-file primary primary.csv --csv-file nuclei nuclei.csv --s3-prefix  s3://starfish.data.spacetx/osmFISH/formatted/20190626/ --tile-width 2048 --tile-height 2048 -o output