Migration to v2 version¶
Neuron
object now extendsmorphio.Morphology
.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. UseSection
instead as it includes its functionality but if you needTree
separately then copy-pasteTree
code from v1 version to your project.Section
andNeurite
class can’t be copied anymore because their underlying MorphIO objects can’t be copied (pickled). Only copying ofNeuron
is preserved.drop
FstNeuron
. It functionality is included inNeuron
class. UseNeuron
instead ofFstNeuron
.- Validation of morphologies changed.
The following is not an invalid morphology anymore: - 2 point soma - non-sequential ids
- script
morph_check
andmorph_stats
changed toneurom check
andneurom stats
correspondingly.
- script