fissa.readimagejrois module#

Tools for reading ImageJ files.

Based on code originally written by Luis Pedro Coelho <luis@luispedro.org>, 2012, available at https://gist.github.com/luispedro/3437255, distributed under the MIT License.

Modified

2014 by Jeffrey Zaremba (@jzaremba), https://github.com/losonczylab/sima
2015 by Scott Lowe (@scottclowe) and Sander Keemink (@swkeemink).

fissa.readimagejrois.parse_roi_file(roi_source)#

Parse an individual ImageJ ROI.

Parameters

roi_sourcestr or file object: Path to file, or file object containing a single ImageJ ROI.

Returns

dict: Returns a parsed ROI object, a dictionary with either a "polygons" or a "mask" field.

Raises

IOError: If there is an error reading the roi file object.
ValueError: If unable to parse ROI.

fissa.readimagejrois.read_imagej_roi_zip(filename)[source]#

Read an ImageJ ROI zip set and parse each ROI individually.

Parameters

filenamestr: Path to the ImageJ ROis zip file.

Returns

roi_listlist: List of the parsed ImageJ ROIs.

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