COSMOS

COSMOS LINK

This website contains instructions for setting up Cortical Observation by Synchronous Multifocal Optical Sampling (COSMOS).

Software repository for processing and analyzing COSMOS data
CAD files and bill of materials for building COSMOS macroscope
Protocol and images describing surgical procedure for implanting curved cranial window
Processed data from imaging sessions used in the manuscript

Kauvar IV*, Machado TA*, et al. Cortical observation by synchronous multifocal optical sampling reveals widespread population encoding of actions, Neuron (2020), https://doi.org/10.1016/j.neuron.2020.04.023.

Abstract: To advance the measurement of distributed neuronal population representations of targeted motor actions on single trials, we developed an optical method (COSMOS) for tracking neural activity in a largely uncharacterized spatiotemporal regime. COSMOS allowed simultaneous recording of neural dynamics at ∼30 Hz from over a thousand near-cellular resolution neuronal sources spread across the entire dorsal neocortex of awake, behaving mice during a three-option lick-to-target task. We identified spatially distributed neuronal population representations spanning the dorsal cortex that precisely encoded ongoing motor actions on single trials. Neuronal correlations measured at video rate using unaveraged, whole-session data had localized spatial structure, whereas trial-averaged data exhibited widespread correlations. Separable modes of neural activity encoded history-guided motor plans, with similar population dynamics in individual areas throughout cortex. These initial experiments illustrate how COSMOS enables investigation of large-scale cortical dynamics and that information about motor actions is widely shared between areas, potentially underlying distributed computations.

LINK to 2020 Neuron research article, Supplementary information

Software

See code at

https://github.com/deisseroth-lab/cosmos-tools

Hardware

Bills of Material and CAD files (for ordering through protolabs)

Please click to access the Google Drive files

Instructions for ordering custom components (mouse headbar, lenslet holder, mouse headbar clamp)

The main things you will likely need to order are headbars (headplate_ring_13mm_tab_shelf_v13.ipt) and the lenslet holder (20171214_lenslet_holder_v10_final.ipt).

For the headbar clamp, you will need to order 2x each of HeadPostHolderBottom.ipt and HeadPostHolderBottom.ipt

Make an account on www.protolabs.com
Click 'Get a Quote' ---> CNC Machining
Upload the ipt CAD file. If you want stainless steel as the material, then you need to click the 'hard metals' option (aluminum is cheaper and faster, and honestly, is probably adequate). Note: you will be able to adjust quantities later.
Submit the quote request.
When the quote comes back (it needs to be approved by protolabs; this takes about a day), for the headbar, you will likely want to thread the two holes on the tabs. In the quote interface, under 'threading options', select the two tab holes and select 4-40 threading. When manufacturing the HeadPostHolderBottom, you will also need to thread the holes to 8-32 threading.

Instructions for ordering curved windows:

Our windows were procured through two vendors: trapezoidal glass blanks were cut by TLC International (contact: clinden@tlcinternational.com), these were then shipped to Glaswerk (maik@glaswerk.com) where they were curved along a 10 mm radius.
You can now buy windows directly through Labmaker: https://www.labmaker.org/products/crystal-skull. These windows are slightly smaller than the ones we used, but should be adequate.

Instructions for making custom lenslets:

Our lenslets were modified Edmund Optics 25 mm Diameter x 40 mm EFL Aspherized Achromatic lenses ( #49-664)
We milled off 7.09 mm from the edge of each of two lenslets (using the Ginzton Crystal Shop at Stanford University, managed by Tim Brand, currently at https://www.brandlaseroptics.com/about --- this should be an easy job for any crystal shop)