MouseLight reconstructions

[hypercompetent]

Add functions to draw MouseLight reconstructions into the 3D brain plots. These can be downloaded in SWC format: http://research.mssm.edu/cnic/swc.html

[FedeClaudi]

Hi,

The link above just brings me to the home page: https://icahn.mssm.edu/ Where can I find the downloadable data?

Also, is there also a way to download the MouseLight data as JSON?

[hypercompetent]

Here's a different page with the SWC spec: http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html

I haven't dug into it yet, but it looks like they may only be available as SWC. Here's the function in mouselightr that retreives the SWC files: https://github.com/natverse/mouselightr/blob/master/R/fetch.R

I'm having trouble tracking down API documentation for these direct queries to MouseLight.

Alternately, it looks like neuromorpho.org has these files as well, with a pretty simple url scheme: http://neuromorpho.org/dableFiles/mouselight/Source-Version/AA0257.swc

Where AA0257 is the MouseLight ID.

[FedeClaudi]

That's great, I wasn't aware of neuromorpho.

It seems that parsing SWC files is quite easy, but unlike the JSON they don't contain the allenID value for each sample [which can be used to reconstruct in which brain region the sample is].

Thanks for the help though!

[anirban6908]

Hi @hypercompetent Would it be possible to add allen institute swc files in the mouse brain mesh. For example can we add this morphology to the atlas? Or they are not mapped to CCF? Thanks

[FedeClaudi]

Hi,

I have a similar problem in python (I've added a question on the community forum.

I can render the .swc in pythons (adding it to BrainRender), but they are not aligned to the CCF. In the python Allen SDK, the Morphology class has a method to apply an affine transform to the coordinates, but I don't seem to find a way to get the correct affine matrix.

Any help would be exceedingly useful!