roifile

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.

.. _ImageJ: https://imagej.net

:Author: Christoph Gohlke <https://www.cgohlke.com>_ :License: BSD 3-Clause :Version: 2024.9.15 :DOI: 10.5281/zenodo.6941603 <https://doi.org/10.5281/zenodo.6941603>_

Quickstart

Install the roifile package and all dependencies from the Python Package Index <https://pypi.org/project/roifile/>_::

python -m pip install -U "roifile[all]"

View overlays stored in a ROI, ZIP, or TIFF file::

python -m roifile file.roi

See Examples_ for using the programming interface.

Source code, examples, and support are available on GitHub <https://github.com/cgohlke/roifile>_.

Requirements

This revision was tested with the following requirements and dependencies (other versions may work):

• CPython <https://www.python.org>_ 3.10.11, 3.11.9, 3.12.5, 3.13.0rc2
• Numpy <https://pypi.org/project/numpy/>_ 2.2.1
• Tifffile <https://pypi.org/project/tifffile/>_ 2024.8.30 (optional)
• Matplotlib <https://pypi.org/project/matplotlib/>_ 3.9.2 (optional)

Revisions

2024.9.15

• Improve typing.
• Deprecate Python 3.9, support Python 3.13.

2024.5.24

• Fix docstring examples not correctly rendered on GitHub.

2024.3.20

• Fix writing generator of ROIs (#9).

2024.1.10

• Support text rotation.
• Improve text rendering.
• Avoid array copies.
• Limit size read from files.

2023.8.30

• Fix linting issues.
• Add py.typed marker.

2023.5.12

• Improve object repr and type hints.
• Drop support for Python 3.8 and numpy < 1.21 (NEP29).

2023.2.12

• Delay import of zipfile.
• Verify shape of coordinates on write.

2022.9.19

• Fix integer coordinates to -5000..60536 conforming with ImageJ (breaking).
• Add subpixel_coordinates in frompoints for out-of-range integer coordinates.

2022.7.29

• …

Refer to the CHANGES file for older revisions.

Notes

The ImageJ ROI format cannot store integer coordinate values outside the range of -5000..60536.

Refer to the ImageJ RoiDecoder.java <https://github.com/imagej/ImageJ/blob/master/ij/io/RoiDecoder.java>_ source code for a reference implementation.

Other Python packages handling ImageJ ROIs:

• ijpython_roi <https://github.com/dwaithe/ijpython_roi>_
• read-roi <https://github.com/hadim/read-roi/>_
• napari_jroitools <https://github.com/jayunruh/napari_jroitools>_

Examples

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

roi = ImagejRoi.frompoints([[1.1, 2.2], [3.3, 4.4], [5.5, 6.6]]) roi.roitype = ROI_TYPE.POINT roi.options |= ROI_OPTIONS.SHOW_LABELS

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

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

Read the ImageJ ROI from the file and verify the content:

roi2 = ImagejRoi.fromfile('_test.roi') roi2 == roi True roi.roitype == ROI_TYPE.POINT True roi.subpixelresolution True roi.coordinates() array([[1.1, 2.2], [3.3, 4.4], [5.5, 6.6]], dtype=float32) roi.left, roi.top, roi.right, roi.bottom (1, 2, 7, 8) roi2.name = 'test'

Plot the ROI using matplotlib:

roi.plot()

Write the ROIs to a ZIP file:

roiwrite('_test.zip', [roi, roi2], mode='w')

Read the ROIs from the ZIP file:

rois = roiread('_test.zip') assert len(rois) == 2 and rois[0] == roi and rois[1].name == 'test'

Write the ROIs to an ImageJ formatted TIFF file:

import tifffile tifffile.imwrite( ... '_test.tif', ... numpy.zeros((9, 9), 'u1'), ... imagej=True, ... metadata={'Overlays': [roi.tobytes(), roi2.tobytes()]}, ... )

Read the ROIs embedded in an ImageJ formatted TIFF file:

rois = roiread('_test.tif') assert len(rois) == 2 and rois[0] == roi and rois[1].name == 'test'

View the overlays stored in a ROI, ZIP, or TIFF file from a command line::

python -m roifile _test.roi

For an advanced example, see roifile_demo.py in the source distribution.