About the Neuromorphological File Specification category

Neuromorphological File Specification
#1

Introduction to the Neuromorphological File Format

Ask questions related to Neuromorphological file format.
MBF Bioscience has chosen to openly document their digital reconstruction file format, Neuromorphological File Specification (4.0), available at www.mbfbioscience.com/filespecification (Angstman et al. 2020). The structures represented have been continually developed for over 30 years, balancing accurate 3D representation of microscopic structures with the efficiency for reading, writing, storing, and rendering the reconstruction data. The neuromorphological file format balances structure with flexibility by storing each modeled object as a unique data element, and providing mechanisms for grouping any number and type of data elements. File-level metadata is retained to provide detail on the origin of the sample, ensuring that the provenance of derivative data is tracked and that important source information is not separated from the corresponding data. The decision to implement each neuromorphological structure, from spines to varicosities, was influenced by top neuroscientists who sought to maintain a meaningful model and have the necessary analysis options for that entity. The file specification has evolved with academia and discovery, and will continue to be updated as needed to define added or modified data elements.

#2

Is documentation available for the Neurolucida Neuromorphology V3 text file written for MicroBrightField products (asc file extension)?

#3

Hi Tom,

MBF Bioscience does not have any documentation for the specific format you mention above (ASC v3). I would recommend that you save the tracings in the ASC format to the XML format using the Neurolucida software. To do this:

  1. Open the data file in Neurolucida
  2. Select File < Save As <Data File. This will open the Save As window.
  3. In the Save As window, choose the file type you would like to save as from the Save as type drop-down menu.
  4. Select the XML (*.xml) file time from the dropdown and click Save.

You can then use the Neuromorphological File Specification (4.0), available at www.mbfbioscience.com/filespecification, to interpret your file’s data elements.

Hope this is helpful!
Aidan

#4

We are using the BluePyOpt optimizer via the HH NEURON builder interface for modeling the voltage and calcium concentration of pyramidal neurons. This software requires a MicroBrightField V3 asc file for defining the morphology of the model. We have models instantiated in NEURON that we would like to export to asc. We tried writing code guessing the format and got part of the way to the solution. It would be nice for developing/debugging to know the V3 asc specification.