This software was written for Matlab 2014b

It requires Matlab software as well as the imaging processing, optimization toolbox and statistics toolbox

(1) Open matlab
(2) Type guide onto the command line, enter
(3) Open the IOS_Software.fig
(4) Activate the software (play button)
(5) Load tiff files for an acquisition using the imgLoad button
(5.5) If using a tiff z-stack click z_stack_one plane to combine the z-stack into a single plane. We used 5 planes in our experiments (planeN = 5). If not go directly to step 6.
(6) Click on “one Button” to register and convert tiff stack into to a mat colormap
(7) Choose color map under clrma, the default is gray, jet was used in the paper
(8) To display increases in calcium click combined “images_NOBlue”
(9) Check eval? to see changes clearly

The software is set for a tiff stack of 70 frames (7s). The pre-stimulus time is 20 frames (2s).

The pre stimulus and binning of the color map overlay can be changed under raw IOS save in mat

The software saves the registered images, the mat colormaps and the combined images in the folder with the original tiff files.