AllenInstitute / AllenInstitute/bmtk

Problem in building a one compartment or several compartments cell

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Python
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Description

Hello, I try to use BMTK to build a one compartment cell, I deleted all lines in morphology file except the first line for soma:

1 1 356.5848 666.8376 28.56 6.4681 -1

it comes the error:

NEURON: x : object prefix is NULL
near line 0
^
Import3d_SWC_read[0].mksections()
Import3d_SWC_read[0].input("./biophys_...")
Biophys1[0].init("./biophys_...")

If I left two more lines in .swc file to build a two compartments cell:

1 1 356.5848 666.8376 28.56 6.4681 -1
2 3 354.1858 672.2133 28.4684 0.1608 1

It comes another error:

NEURON: section in the object was deleted
near line 0
{soma { pt3dadd(363.053, 666.838, 28.56, 12.9362) }}
^
*** longjmp causes uninitialized stack frame ***:

This is my method to build the network:

net = NetworkBuilder('BL')
net.add_nodes(cell_name='BL',
potental='exc',
model_type='biophysical',
model_template='ctdb:Biophys1.hoc',
model_processing='aibs_perisomatic',
dynamics_params='fit_parameters.json',
morphology='reconstruction.swc')
net.build()
net.save_nodes(output_dir='network')

How to solve these problems and is there any right way to build a one compartment or several compartments cell?

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start at the NetworkBuilder call in the issue and inspect how ctdb:Biophys1.hoc processes reconstruction.swc and fit_parameters.json. Reproduce the one- and two-compartment cases using the shown morphology lines, then verify that net.build() and net.save_nodes(output_dir='network') complete without the reported NEURON errors.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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