File Formats

Input File Formats

Ultraliser has native support to read and write different types of data (meshes, volumes, images, image stacks and morphological skeletons) in several file formats. In this page, the user can find a comprehensive summary of all the file formats that can be read or written by Ultraliser.

Input Meshes

The current version of Ultraliser is capable of reading polygonal surface meshes with the following file formats:

• Wavefront object .OBJ files.
• Polygonal file format .PLY files in ASCII encoding.
• Stereolithography file format .STL files.
• Object file format .OFF files.
• .H5 files: a custom format that was created by the MICrONS consortium to store the segmented meshes from their cortical dense reconstructions. The vertices and triangles are created into two different HDF5 groups. We implemented a specific reader to load those H5 meshes to directly convert all the reconstructions produced by the MICrONS consortium.

NOTE: If the input mesh has N-gons, where N > 8, the current version of Ultraliser will NOT be capable of reading it. Therefore, it is recommended to triangulate this mesh in MeshLab or Blender and then load it in Ultraliser.

NOTE: All the generated surface meshes with Ultraliser are triangular, i.e. composed of triangular patches only.

Input Volumes

The current version of Ultraliser is capable of reading volumes with the following file formats:

• Nearly raw raster data files in .NRRD format.
• Ultraliser-based volume files in .UVOL format.
• Raw volumes with seperate header file in .HDR/.IMG format. The .HDR file contains the type and dimensions of the data in ASCII encoding, while the .IMG file contains a raw sequence of binary values representing the volume data.

Input Morphologies

The current version of Ultraliser is capable of reading morphological skeletons of neurons, astrocytes and vasculature networks in several standard and customized file formats.

Neuron Morphologies

Ultraliser can read neuron morphologies in the following file formats:

• The standard .SWC format adopted by NeuroMorpho.Org.
• The BBP- and HBP-specific file format .H5. This format is read by other applications like NeuroMorphoVis, NeuroM and MorphIO.

Sample datasets can be found at the following data repositories:

• NeuroMorpho.Org
• NeuronDB
• NeuroMorphoVis

Astrocyte Morphologies

Compared to neurons, available reconstructions of astroglial cells are sparse. Even complete astrocytic reconstructions (that have endfeet data) are extremely limited. In fact, NeuroMorpho.Org has ~6,000 astrocytes, but none of them contains any endfeet descriptions; only the arborizations of perisynaptic and perivascular processes. These astrocyte morphologies are basically similar to neuron in their structure; they are also stored in the standard .SWC format that describe arborizations and branching data.

A recent research was published by Zisis et al, where the authors were capable of synthesizing biologically realistic astrocytic morphologies with endfeet data. The synthesis code is still closed source, but we also integrated a script that can create custom .H5 files that contain data of the arborization and endfeet, all integrated in a single file.

In summary, Ultraliser can read astroglial morphologies with the following file formats:

• .SWC
• .H5

Vasculature Morphologies

Currently, and to the best of out knowledge, there is no standard file format for describing the connectivity of vascular networks that are represented by cyclic graphs. Nevertheless, there are a few file formats that are becoming quite common and have been already used by several applications for vasculature visualization, analysis and meshing.

The standard .SWC file format that is mainly used to store branching details of neuronal and astroglial morphologies is used in several contexts to store the connectivity of vascular networks. A workaround is made to represent the loops (cycles). There are several SWC morphology samples available from the Brain Vasculature (BraVa) database. The Brain Vasculature (BraVa) database contains digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs).

A recent tool called VessMorphoVis was designed to visualize, analyse and mesh vascular morphologies. This tool introduced a new file format called .VMV. Ultraliser has full native support to load VMV files.

Ultraliser also supports loading H5 morphology files that are designed for internal usage by the Blue Brain Project.

In summary, Ultraliser can read morphologies of vascular networks with the following file formats:

• .SWC
• .VMV
• .H5

Output File Formats

Similarily, Ultraliser generates different types of data (meshes, volumes, projections, statistical analysis data) in several file formats.

Output Meshes

The current version of Ultraliser is capable of writing triangular surface meshes with the following file formats:

• Wavefront object .OBJ files.
• Polygonal file format .PLY files in ASCII encoding.
• Stereolithography file format .STL files.
• Object file format .OFF files.

It can export meshes to the following items

• structure
• Bounding Volumes
• Volume Grids

Output Volumes

The current version of Ultraliser is capable of writing volumes with the following file formats:

• Nearly raw raster data files in .NRRD format.
• Ultraliser-based volume files in .UVOL format.
• Raw volumes with seperate header file in .HDR/.IMG format. The .HDR file contains the type and dimensions of the data in ASCII encoding, while the .IMG file contains a raw sequence of binary values representing the volume data.

Output Images

The current version of Ultraliser is capable of writing images (mainly projection images) in the following file format(s):

• Portable Pixmap Format .PPM.