Imalytics Preclinical uses the GFF format (.gff) by default to load and save underlay, overlay, segmentation, and project files. The file format supports multimodal and time-variant images and it utilizes a lossless compression algorithm to reduce file size. Furthermore, a rich set of metadata is contained in the header and cryptographic hashing secures reading and writing.
If you want to learn more about GFF, please refer to the publication by Grace et al. (full text here).
Gremse-IT has published an open source python package called gffio to provide an interface between Imalytics Preclinical and Python. The package enables Python users to load .gff files into their existing image preprocessing pipeline by converting the underlying data to numpy arrays. Additionally, the metadata can be read and modified. Importantly, the package offers functions to save five-dimensional arrays with optional metadata as a .gff file for visualization and further analysis in Imalytics Preclinical.
You can find the public Git repository with installation instructions here.
The repository also contains Jupyter notebooks explaining the basic usage of the package and showcasing some exemplary image processing methods. Further tutorials will be added in the future.
If you have any questions regarding gffio, please contact us at info@gremse-it.com. We are happy to help you automate your image processing needs!