2023 CCN Workshop on Calcium & Imaging Voltage Analysis
Workshop Description
New imaging modalities - including endoscopic and multiphoton calcium imaging, and single and multiphoton voltage imaging, among others - have granted unprecedented access to the activity of large neuronal populations with high temporal resolution. As such, those methods have been instrumental in obtaining new neurobiological insights inaccessible to other recording modalities. However, the barrier to establishing reproducible and efficient computational pipelines for imaging datasets, along with the difficulty of integrating this technology into real-time experiments, have substantially slowed progress in neuroscience and represent a significant opportunity cost for many laboratories.
CaImAn is an open-source software platform that provides optimized and scalable routines to process imaging data with the goal of extracting the activity of each neuron. CaImAn handles multiple imaging modalities (voltage, calcium, endoscopic, multiphoton, volumetric) and analysis settings (batch/offline vs online/real-time). Mesmerize is a new organizational and visualization framework that allows for efficient and streamlined analysis using CaImAn algorithms, and enables users with minimal programming experience to use CaImAn effectively. CaImAn is very popular among neuroscientists world-wide, but its widespread dissemination, the efficient use of its routines, and the opportunities provided by Mesmerize, require access to training opportunities. We will address this challenge by establishing a workshop at the Flatiron Institute, Simons Foundation.
The free workshop will be of interest to imaging researchers at many levels of experience. It will provide a unique opportunity to directly learn from lead developers of both CaImAn and Mesmerize for analysis of calcium and voltage data. Attendees will receive:
Tutorials on cutting edge calcium and voltage imaging analysis tools.
Hands-on training with real data sets and practical code examples that they will be able to use with their own data.
Receive training on the new Mesmerize framework for batch analysis and data organization enabling streamlined use of CaImAn algorithms.
Training on the mesmerize-viz and fastplotlib libraries for very fast visualization or large-scale datasets in Jupyter notebooks.
More experienced users and developers will have the opportunity to participate in a hackathon, make contributions to the core packages, and become active contributors to these tools moving forward.
Training in DataJoint: data organization and infrastructure with the help of a database server.
Application Deadlines
Workshop attendance will be capped at 30 attendees. In the event that there are over 30 applications, participation will be restricted to one applicant per lab. Applications to attend the workshop will be accepted through midnight on Sunday, November 6, and admitted attendees will be notified by Friday, November 18; persons who applied for travel grants will also be notified by November 18.
If your application is accepted, you will be required to submit your intent to attend by Tuesday, November 22 to help ensure full attendance and to allow time for travel arrangements.
The event will also be recorded as a reference for attendees, and for those who are unable to attend.