data and supplement: stage top fluorescent microscopy calcium imaging and optogenetics validation

stabilizedGCaMPCHRmine3.zip – Archive containing a folder of TIFF images processed to reduce drift and improve signal-to-noise ratio. The data were downsampled to 12 FPS (half the original 24 FPS) and scaled to 50% of the original dimensions to accommodate hardware limits when processing thousands of frames. The raw, unstabilized data are provided separately. Processing in ImageJ involved: opening the TIFFs as an image stack, selecting the central four minutes of stable recording, adjusting contrast automatically, applying a despeckle filter to enhance signal-to-noise, and using the Template Matching plugin to correct drift. This stabilized stack is the content of the compressed file. chrmine3ROIs.png – Derived from the stabilizedGCaMPCHRmine3 image stack. A standard deviation projection over time was generated to identify regions of putative neuronal activity. These regions of interest (ROIs) are circled and correspond to the ROIs referenced in the thesis. ChRmine3StabilizedROIs.csv – Output from ImageJ’s ROI analysis, containing the average pixel intensity traces for each ROI along with selected baseline periods. gcampChrmine3.zip – The raw data set from which stabilizedGCaMPCHRmine3 was generated. Recorded at 24 FPS using a Basler Dart camera (daA1280-54uc).