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
| Application | Use it for | Launch command |
|---|---|---|
| Viewer | Overlay images, channels, masks, points, and transformations | i2viewer |
| Register | Manually align two images with fiducial markers | i2register |
| Elastix | Register whole-slide images with Elastix workflows | i2elastix |
| Valis | Register whole-slide images with Valis workflows | image2image -t valis |
| Runner | Queue and review multiple registration projects | i2runner |
| Convert | Convert supported microscopy formats to OME-TIFF | i2convert |
| Crop | Crop or mask one or more images | i2crop |
| Merge | Combine channels or image files | image2image -t merge |
| Fusion | Export data for the MATLAB fusion application | image2image -t fusion |
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
- Open the Viewer to inspect your images and confirm their pixel sizes.
- Use Register to create an affine transformation between two modalities, or choose Elastix or Valis for whole-slide registration.
- Review the alignment and export the resulting images or transformation files.
- 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.
1 maintainer
Metadata
1 maintainer
Release files for image2image 0.3.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| image2image-0.3.1.tar.gz | 361.3 kB | Without provenance | Details for image2image-0.3.1.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| image2image-0.3.1-py3-none-any.whl | Python 3 | none | any | Details for image2image-0.3.1-py3-none-any.whl |
Total release size: 753.4 kB
Release files / image2image-0.3.1.tar.gz
| Download URL | image2image-0.3.1.tar.gz |
|---|---|
| Size | 361.3 kB |
| Tags | Source |
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Release files / image2image-0.3.1-py3-none-any.whl
| Download URL | image2image-0.3.1-py3-none-any.whl |
|---|---|
| Size | 392.0 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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Security for image2image 0.3.1
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