roifile 2024.9.15

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

License:

BSD 3-Clause

Version:

2024.9.15

DOI:

10.5281/zenodo.6941603

Quickstart

Install the roifile package and all dependencies from the Python Package Index:

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.

Requirements

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

• CPython 3.10.11, 3.11.9, 3.12.5, 3.13.0rc2

• Numpy 2.2.1

• Tifffile 2024.8.30 (optional)

• 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 source code for a reference implementation.

Other Python packages handling ImageJ ROIs:

• ijpython_roi

• read-roi

• 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.