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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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