Migration to v2 version¶
Neuronobject now extends
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
neurom.check.structural_checksas MorphIO does not allow to load invalid morphologies, and it does not give access to raw data.
Sectioninstead as it includes its functionality but if you need
Treeseparately then copy-paste
Treecode from v1 version to your project.
Neuriteclass can’t be copied anymore because their underlying MorphIO objects can’t be copied (pickled). Only copying of
FstNeuron. It functionality is included in
- Validation of morphologies changed.
The following is not an invalid morphology anymore:
2 point soma