Endoplasmic reticulum

Endoplasmic reticulum can also be stored and written to H5 file. The specification is part of the BBP morphology documentation There is one endoplasmic reticulum object per morphology. It contains 4 attributes. Each attribute is an array and each line refers to the value of the attribute for a specific neuronal section.

  • section_index: Each row of this dataset represents the index of a neuronal section. Each row of

    the other properties (eg. volume) refer to the part of the reticulum present in the corresponding section for each row.

  • volume: One column dataset indexed by section_index. Contains volumes of the reticulum per each

    corresponding section it lies in.

  • surface_area: Similar to the volume dataset, this dataset represents the surface area of the

    reticulum in each section in the section_index dataset.

  • filament_count: This 1 column dataset is composed of integers that represent the number of

    filaments in the segment of the reticulum lying in the section referenced by the corresponding row in the section_index dataset.

Reading endoplasmic reticula from H5 files

from morphio import Morphology

morpho = Morphology('/my/file')
reticulum = morpho.endoplasmic_reticulum
print('{indices}, {volumes}, {areas}, {counts}'.format(

Writing endoplasmic reticula from H5 files

neuron = Morphology()

reticulum = neuron.endoplasmic_reticulum
reticulum.section_indices = [1, 1]
reticulum.volumes = [2, 2]
reticulum.surface_areas = [3, 3]
reticulum.filament_counts = [4, 4]
neuron.write('/my/out/file.h5')  # Has to be written to h5