How to obtain all the synaptic data of a specific brain region in mice

Technical
1

I want to obtain the data of all the synapses in the mouse olfactory bulb, cerebral cortex, and hippocampus regions (I only want to know the connection situation between the synapses). I noticed that the “MICrONs Tutorial - Synaptic Connectivity” webpage provides the CAVE engine, which can be used to query synapse data. However, the query method is through root IDs, but I don’t know the root IDs of the synapses in the brain regions I’m interested in, and I haven’t found a way to query the IDs of synapses in specific brain regions. Therefore, I considered another method. I observed that the “s
ynapse_query” library function provided by CAVE offers bounding_box filtering queries. So, I thought that if I knew the approximate bounding_box range of the three brain regions, I could roughly obtain the synapse data of these regions. However, when I observed the 3D model you provided at the “3d Viewer :: Allen Brain Atlas: Mouse Connectivity” website, I could get the approximate coordinate range of specific brain regions from it, but I don’t know what the unit is. Based on my judgment, I think it is micrometers. However, the position coordinates of the synapses in the synapses_pni_2 data provided by the CAVE engine are inconsistent with those in the 3D model. I think the unit is nanometers or voxels (4×4×40 nanometers). After converting the units and using the bounding_box to query the synapses, I couldn’t find any synapses. So, I think these two coordinate systems are not the same. Is that correct?

Therefore, I would like to ask how I can obtain the synapse data of specific brain regions. Is there a way to get the root IDs of the synapses in specific brain regions or how can I know the 3D coordinate range of specific brain regions so that I can query the synapses of that brain region through the bounding_box?

2

Hi,
Thank you for your question.
Below is a response from one of our scientific team member experts.

The Connectome Annotation Versioning Engine (CAVE) tooling is specific to certain datasets. Right now, that is just the MICrONS electron microscopy reconstruction of mouse visual cortex.The coordinates are aligned to the dimensions of the dataset (here a cubic millimeter EM block), and not to the Allen Brain Atlas common coordinate framework (CCF).

MICrONS does offer detailed synaptic connectivity of tens of thousands of cells, and hundreds of millions of synapses. But all of this is within mouse visual cortex (VISp, VISrl, VISlm).

We do not have an electron microscopy dataset of other brain regions at this time, and so we do not have the same level of detailed synaptic connectivity in hippocampus or olfactory bulb. If you would like to know more about the MICrONS connectivity data, we can direct you to specific resources.

The MICrONs Tutorial - Synaptic Connectivity is a good option. See also the Connectivity viewer ; and scientific support from the VORTEX project