read-roi

Read ROI files .zip or .roi generated with ImageJ. Code is largely inspired from : http://rsb.info.nih.gov/ij/developer/source/ij/io/RoiDecoder.java.html

Functions

from read_roi import read_roi_file
from read_roi import read_roi_zip
from read_roi import read_roi_bytearray

roi = read_roi_file(roi_file_path)

# or

rois = read_roi_zip(roi_zip_path)

# or
import tifffile

with tifffile.TiffFile('path/to/file.tif') as tif:
    s = tif.imagej_metadata
    name = tif.filename
    for imageJ_roi in s['rois']:
        rois = read_roi_bytearray(imageJ_roi, name)

Note

• Some format specifications are not implemented. See RoiDecoder.java for details.
• Most of "normal" ROI files should work.
• Feel free to hack it and send me modifications.

Requirements

• Python 3.6 and above.

Install

pip install git+https://github.com/bjarne89/read-roi

License

Under BSD license. See LICENSE.

Authors

• Hadrien Mary hadrien.mary@gmail.com
• Bjarne Kvæstad bjarnekvae@gmail.com