AllenInstitute / AllenInstitute/bmtk
Synapse location
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- Dominant language
- Python
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Description
Hi,
I am currently working on a project that I want to put all synapse on a particular segment of the dendrite.
I find the https://alleninstitute.github.io/bmtk/bionet.html says there is an option to use “afferent_section_id” and “afferent_section_pos” to pinpoint the location of the synapse. Is there any example of such a usage?
Also, when I look at the file structure, there is no file saving the segment structure from Neuron, does that mean there is a chance Neuron can parse the morphology differently and make the pre-assigned segment-id not work?
Thanky you for the BMTK and thank you for answering the question,
Yuan-Ting Wu
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 with bionet.html and the usage of afferent_section_id and afferent_section_pos mentioned in the issue; compare any existing examples and the morphology or segment handling described there. Done would be a documented example and a clear explanation of whether NEURON can preserve the assigned segment IDs.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100