One-photon calcium imaging in the object space task
Field of View from a 1-p imaging experiment
Average image form one photon microspy in a freely moving mouse.
Here you can see the different components that are extracted after model optimazation using CNMF-e: original video, source extracted signals, background and noise.
Preprocessing videos using CaImAn
We use CaImAn ( Giovanucci, et all. e-Life 2019 : CaImAn an open source tool for scalable calcium imaging data analysis) to preprocess images from Inscopix microscope.
Source extraction from miniscope
We optimaze the extraction output by selecting optimal initial conditions that give a resonable number of cells.
Example of temporal traces extracted from multiple sources
Tracking cells during multiple trials, sessions and days
Different videos from multiple trials are concatenated and aligned together to be able to keep track of the same sources during long time intervals. Here an example of a source active during a resting period and a running period.
Example of tracking of multiple cells after registration and template matching. Different frames are different trials in the experiment, with resting periods in between.
Studying Sources Activity
Heatmap for calcium imaging activity
Single cell activity aligned to behavioural onset, this is equivalent to a raster plot but with calcium temporal traces.