CSM Optogenetics Platform

Light-based molecular tools to visualize and manipulate the brain in animal models.

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The CSM Optogenetics Platform’s goal is to offer an array of equipment and facilities for the combined use of optogenetic stimulation, fiber photometry, and head-mounted miniscopes, with behavioural testing in mice and rats.

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Principle Investigators are required to sign a service agreement. Access to our booking system and card access to the facility is given after users receive an orientation.

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Staff scientists, facility specialists, and management involved in the daily operations.

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Our platform facilitates research that ends up in peer-reviewed journals. Check-out the most recent publications.

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Equipment and fees

Hourly rates are applied according to the equipment/room used up to a yearly cap.

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Useful resources including optogenetics and data analysis presentations and tutorials

Open Neuroscience - Innovative Research Tools

Our team is actively involved in research and developing innovative solutions for data processing and analysis, in addition to developing customized and integrated hardware/software solutions not found commercially.

Visual Gait Lab

Gait Analysis

Crowdsource annotation tools

Crowdsource annotation tools

EMG and fiber-photometry analysis pipeline

EMG and fiber-photometry analysis pipeline

DAQ synchronization

DAQ synchronization

Homecage wheel

Homecage wheel

Walkway setup for gait analysis

Walkway apparatus

Custom-made solutions

Plugins, macros, others

  • ImageJ/FIJI StackRoi: Automatic duplication of ROIs in a image stack.

  • WholeBrain WholeBrainSorter: Master spreadsheet with cell counts from all brain regions.

  • Deeplabcut: Segmentation of behavioral data (soon).

Workshop tools

  • 3D printers

  • CO2 laser cutting machine

  • Rotary tool kit

  • Soldering station

Workshop micro-controllers and sensors

  • Arduino

  • Raspberry Pi

  • Nordic semiconductor

  • High-speed cameras, thermal camera, accelerometer, etc.

Learning Resources


MATLAB tutorials

MATLAB video tutorials for the purposes of looking at neural dynamics using imaging techniques such as fibre-photometry and miniscope recordings, both of which CSMOpto CORE has available for you.

Open video tutorials

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Optogenetic techniques

Here's a link to SfN’s Optogenetics Training Series for those of you interested in advancing your understanding of how to optimize optogenetic techniques in your research.

Open course (external)

Animal Behavior Tracking with ANY-maze

Anymaze tutorials

Video tutorials for learning ANY-maze software.

Open video tutorials