roifile 2020.5.1

Read and write ImageJ ROI format

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

Version:

2020.5.1

Requirements

• CPython >= 3.6

• Numpy 1.15.1

• Tifffile 2020.2.16 (optional)

• Matplotlib 3.1 (optional)

Revisions

2020.5.1

Split positions from counters.

2020.2.12

Initial release.

Notes

Other Python packages handling ImageJ ROIs:

• ijpython_roi

• imagej-tiff-meta

• read-roi

Examples

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 bytes or file:

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

Read the ImageJ ROI from the file:

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

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.