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Systems Club I – Calcium Imaging Pipeline:

From Data Acquisition to Analysis

April 29, 2022 @ 2:00 pm 7:00 pm

The field of optical calcium imaging, particularly of individual neuron function in the intact tissue, relies on detecting subtle changes in light intensity. The implementation of 2-photon microscopy in combination with calcium indicators allowed for the first time a functional readout of neuronal circuits comprising of several hundred neurons in the rodent cortex. This led to a tremendous advance in our understanding on how complex circuit dysfunction arise, particularly also in early stages of neurological disorders. Particularly 2 photon calcium imaging approaches pose unique challenges, both in terms of system integration, experimental design, and not the least, analysis. Most of these steps are processed quite differently depending on the laboratory. Here, in a hands-on-manner, we aim to show you our procedure of data acquisition and analysis, including the GUI ViNe-Seg, which has been recently developed in the Stroh-Lab.

In our Systems Clubs we want to encourage you to join the discussion. Bring your own opinions and if you think it is helpful, feel free to bring a short presentation giving a new impulse on the topic at hand. This Systems Club is particularly aiming for initiating a discussion of different procedures for image processing and downstream analyses of calcium imaging data.

The planned time table is the following:

2 – 3:30PM: Welcome, Presentations and Discussion Round on:

  • The Data Acquisition (Hendrik Backhaus)
  • The Autosegmentation, Trace Extraction, Baseline Estimation and Peak Detection (Nicolas Ruffini, Saleh Altahini, Hendrik Backhaus)
  • The Downstream Analysis (Anna Wierczeiko, Nicolas Ruffini)

3:30 – 4:30PM: Short tours showing the Experimental Calcium Imaging Setup in RG Stroh

  • 2-Photon Microscope Tour
  • Miniscope & Electrophysiology Tour

While you are waiting for your next tour slot or if you are already done, you can start joining the catering and open discussion.

4:30PM – Open End: Discussion with Catering and Wine


Registration is available after login – if you do not have an ISyN-Account yet, create one, using the “Become a member”-Button in the top

After you registered for this event, you will get an e-mail asking you for some more details regarding e.g. tours you’d like to participate in.

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Nicolas Ruffini

Biozentrum 1

Hanns-Dieter-Hüsch-Weg 15
Mainz, RLP 55128 Germany