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Matlab scripts for analyzing calcium imaging data presented in "Neural Coding of Leg Proprioception in Drosophila" (Mamiya, Gurung, and Tuthill (2018) Neuron: DOI:https://doi.org/10.1016/j.neuron.2018.09.009)

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MamiyaA/NeuralCodingOfLegProprioception_CalciumImagingAnalyses

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Neural Coding Of Leg Proprioception (Calcium imaging analyses)

Analysis scripts for calcium imaging data presented in the paper "Neural Coding of Leg Proprioception in Drosophila" (Mamiya, Gurung, and Tuthill (2018) DOI:https://doi.org/10.1016/j.neuron.2018.09.009)

Graphical Abstract

All imaging data are multi-channel, time series image acquired using ScanImage Software (Vidrio Technologies)

Brief description of each script:

FilterAndRegisterImages: Separate the signal channel and reference channel in the multi-channel .tiff image, filter each image using Gaussian filter, register the images using 2D fast-fourier transform. Display original and filtered image sequences.

FilterAndRegisterImages_All: Runs FilterAndRegisterImages for all the appropriate files in the directory.

FilterImages: Separate the signal channel and reference channel in the multi-channel .tiff image, filter each image using Gaussian filter. Display original and filtered image sequences.

KmeansClusterPixels: For the pixels inside the preselected region of interest, cluster the pixels into different groups with K-means clustering using the correlation between the pixel's responses to the stimuli as a distance measure. Results in groups of pixels that have similar responses to the stimuli.

KmeansClusterPiexels_All: Runs KmeansClusterPiexels for all the appropriate files in a directory.

SelectROICalculateDFF: Ask the user to manually select ROI, apply predefied pixel intensity threshold for each selected ROI, then calculate the DF/F (change in flureoscence relative to the baseline fluorescence) of those pixels based on the specified baseline frames.

SelectROICalculateDFF_All: Runs SelectROICalculateDFF for all the appropriate files in a directory.

SelectROIManually: Let the user manually select the region of interest to analyze the activity

SelectROIManually_All: Runs SelectROIManually for all the appropriate files in a directory

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