Data Management

How to manage your data in KI-Morph

Importing data

After creating a project, you can add image volumes to it. Multiple volumes can be added to a single project, allowing you to manage and analyze several datasets within the same workspace.

To import data navigate to the dataset page (/SDS-acronym/project-name/segmentation/dataset) and click on the "Add volume" button on the top right. In the dialog that opens, you can choose an id for the volume and then select the data source.

Currently, KI-Morph is targeted at 3D grayscale images. Support for images with more than one channel may be added in the future, expanding the range of data types that can be processed by KI-Morph. The algorithms are all designed to work with images acquired from any imaging technique, such as MRI, CT, or others, and are agnostic to pixel size—whether a pixel represents a nanometer or a kilometer, the platform can handle it. This flexibility allows users to analyze data from a wide variety of sources and scales.

It is important to note that while KI-Morph can process diverse types of images, the accuracy of the results depends on several factors. These include not only the imaging modality and pixel size, but also the quality of image acquisition and how clearly the object of interest is separated from the background. High-quality images with well-defined structures will generally yield better segmentation and analysis outcomes.

You may try z-stacks, i.e., 3D images where the pixels along the z-axis have a larger pixel size than the pixels along the x and y axes. However, as in these images often an significant amount of information is missing between the z-slices, these image are more complex to process, an may lead to worse results.

Supported formats

KI-Morph currently supports importing data from a wide range of formats to accommodate various workflows and imaging modalities:

  • Single TIFF files
  • OME-TIFF files (.ome.tif/.ome.tiff)
  • Folders of TIFF files
  • Zarr stores (.zarr directories)
  • NumPy arrays (.npy)
  • NumPy archives (.npz)
  • HDF5 files (.h5/.hdf5)
  • NIfTI images (.nii, .nii.gz)
  • DICOM files (.dcm) or folders of DICOMs
  • Neuroglancer Precomputed volumes
  • NRRD images (.nrrd)
  • Raw binary volumes (.raw)
  • Archives (.zip, .tar, .tar.gz, .tgz, .tar.bz2, .tbz2, .tar.xz, .txz) that contain one of the supported data types

Exporting data

Navigate to the dataset page and click on the triangle icon to the left of the image you want to export. This will bring up a menu with more information about the image as well as a button to export the segmentation of the image.

Deleting data

At this time, it is not possible to delete data from the platform. This limitation exists due to technical restrictions, as we cannot determine whether the data is being used outside of KI-Morph. If you need to delete data, please contact the KI-Morph team for assistance.