image2image

Explore, align, and prepare scientific images in one place.

image2image is a desktop toolkit for visualizing and registering whole-slide images, microscopy data, and imaging mass spectrometry datasets. It brings a collection of focused applications together behind one launcher, so you can move from inspection to registration to export without changing tools.

Why image2image?

• See multiple modalities together. Overlay images, channels, masks, and point data in a shared viewer, with per-dataset scaling and transformations.
• Register images interactively. Create affine registrations with fiducial points, preview the result, and save reusable transformation files.
• Register whole-slide images. Build Elastix or Valis workflows with preprocessing, masks, registration paths, and batch execution.
• Prepare data for downstream tools. Convert images to OME-TIFF, crop or mask regions, merge channels or files, and export fusion-compatible data.
• Work from the GUI or command line. Use the launcher for a guided workflow, or invoke individual applications from a terminal.

Applications at a glance

The default image2image command opens the launcher, where all available applications can be started.

Install

image2image requires Python 3.11 or newer. Install it from PyPI with a Qt backend, then start the launcher:

python -m pip install "image2image[pyqt6]"
image2image

If you prefer another supported Qt binding, replace pyqt6 with pyside6, pyqt5, or pyside2.

For packaged application builds and release notes, see the GitHub Releases page.

A typical workflow

1. Open the Viewer to inspect your images and confirm their pixel sizes.
2. Use Register to create an affine transformation between two modalities, or choose Elastix or Valis for whole-slide registration.
3. Review the alignment and export the resulting images or transformation files.
4. Use Crop, Convert, or Merge to prepare the final data for analysis or sharing.

Documentation

• Documentation home
• Viewer guide
• Registration guide
• Elastix guide
• Valis guide
• Utility apps
• Release notes

Development

Clone the repository and install the project with its development tools:

git clone https://github.com/vandeplaslab/image2image.git
cd image2image
python -m pip install -e "[pyqt6,dev]"

Contributions are welcome. Please open an issue for a bug report or feature request, or submit a pull request with a focused change and relevant tests.

License

image2image is released under the BSD 3-Clause License.