Migration to v2 version

  • Neuron object now extends morphio.Morphology.

  • NeuroM does not remove unifurcations on load. Unifurcation is a section with a single child. Such sections are possible in H5 and ASC formats. Now, in order to remove them on your morphology, you would need to call remove_unifurcations() right after the morphology is constructed.

    import neurom as nm
    nrn = nm.load_neuron('some/data/path/morph_file.asc')
    nrn.remove_unifurcations()
    
  • Soma is not considered as a section anymore. Soma is skipped when iterating over neuron’s sections. It means that section indexing offset needs to be adjusted by -(number of soma sections) which is usually -1.

  • drop benchmarks

  • drop neurom.check.structural_checks as MorphIO does not allow to load invalid morphologies, and it does not give access to raw data.

  • drop Tree class. Use Section instead as it includes its functionality but if you need Tree separately then copy-paste Tree code from v1 version to your project.

  • Section and Neurite class can’t be copied anymore because their underlying MorphIO objects can’t be copied (pickled). Only copying of Neuron is preserved.

  • drop FstNeuron. It functionality is included in Neuron class. Use Neuron instead of FstNeuron.

  • Validation of morphologies changed.

    The following is not an invalid morphology anymore:

    • 2 point soma

    • non-sequential ids

  • script morph_check and morph_stats changed to neurom check and neurom stats

    correspondingly.