My experiments involve two photon calcium imaging of neurons in vivo, which outputs data as a large time series of individual images (stack). I’ve been using the Multi Measure plugin to select ROIs and get the mean intensity of each ROI at each time point in the stack. The plugin has been working wonderfully for this, however in more recent experiments I am repeatedly imaging from the same area over multiple days. Between days, my scans tend to be off from one another slightly in the XY coordinates. This means my ROI map from the first day does not line up with where the neurons are in the second day scan. While Multi Measure does have a tool to update the position of individual ROIs, I cannot find (in ImageJ or on the internet) a way to shift all of my ROIs at once in the same direction. This is necessary as I am generally dealing with hundreds of ROIs at once, making manually adjusting each ROI prohibitive. Does anyone know of a solution within ImageJ, or alternatively another method such as through MATLAB?
Thanks in advance.
Example of two neurons, green circles indicate ROI position from day one scan, while current neuron position is offset to the right.