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Read and write ImageJ ROI format

Project description

Roifile is a Python library to read, write, create, and plot ImageJ ROIs, an undocumented and ImageJ application specific format to store regions of interest, geometric shapes, paths, text, and whatnot for image overlays.

Author:Christoph Gohlke
Organization:Laboratory for Fluorescence Dynamics, University of California, Irvine
License:BSD 3-Clause



Initial release.


Create a new ImagejRoi instance from an array of x, y coordinates:

>>> roi = ImagejRoi.frompoints([[1.1, 2.2], [3.3, 4.4], [5.4, 6.6]])
>>> roi.coordinates()
array([[1.1, 2.2],
       [3.3, 4.4],
       [5.4, 6.6]], dtype=float32)
>>> roi.left, roi.left, roi.right, roi.bottom
(1, 1, 5, 6)

Export the instance to an ImageJ ROI formatted byte string or file:

>>> out = roi.tobytes()
>>> out[:4]
>>> roi.tofile('_test.roi')

Read the ImageJ ROI from the file:

>>> roi2 = ImagejRoi.fromfile('_test.roi')
>>> roi2 == roi

Plot the ROI using matplotlib:

>>> roi.plot()

To view the overlays stored in a ROI, ZIP, or TIFF file from a command line, run python -m roifile _test.roi.

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