HDF5 Examples

Since MISalign 2.0, datasets in HDF5 files are supported as an alternative data source to image files. The example folder of the git repository contains multiple examples showing how MISalign can be used with HDF5 files, both ones that it created as well as ones from other sources such as NeXus and Dream3D.

Native HDF5 Support

/example/project_a0_hdf5 folder in the git repository.

The example .ipynb includes setting up a MISProjectHDF5 by ingesting image files, adding relations from an existing project, and rendering from the .hdf5 project file. The .mis.hdf5 project file is included in the example folder.

Note: Rather than adding relations from an existing project, this file could be used with notebooks/align.ipynb by changing the MISProjectJSON in the align notebook to MISProjectHDF5.

NeXus Format HDF5 Support

/example/project_a1_nexus folder in the git repository.

The example .ipynb includes building a mock .nxs (using nexusformat and pynxtools) and then doing image dataset discovery from the mock .nxs, constructing a MISProjectJSON with the datasets in the HDF5, adding relations from an existing project, adding scale calibration, and then saving the .mis.json. This .mis.json is suitable for use in notebooks/render.ipynb for rendering from the .nxs file. The .mis.json project file and the .nxs data source are included in the example folder.

Note: Rather than adding relations from an existing project, this file could be used with notebooks/align.ipynb.

Dream3D Format HDF5 Support

/example/project_a2_dream3d folder in the git repository.

The example .ipynb includes building a mock .dream3d (using simplnx) and then doing image dataset discovery from the mock .dream3d, constructing a MISProjectJSON with the datasets in the HDF5, adding relations from an existing project, adding scale calibration, and saving the .mis.json. This .mis.json is suitable for use in notebooks/render.ipynb for rendering from the .dream3d file. The .mis.json project file and the .dream3d data source are included in the example folder.

Note: Rather than adding relations from an existing project, this file could be used with notebooks/align.ipynb.