Removing large scale fluctuations: divide by lowpass

In 1P movies there are enormous fluctuations of background that make viewing and analysis of the movies problematic, especially if you apply dff: (F-F0)/F0.

One option to remove these large scale fluctuation is to take a low-passed frame as F0 for each frame.

Mosaic App: Process -> Movie -> VLM -> Divide by low pass Empirically good value for the radius of the spatial filter is 200 pixels (on full resolution 1P movies).

You need to supply a binary vessel mask to this app. See How to create a mask of vessels for details.

Algorithm:

• Image is extrapolated into the vessel regions as defined by the mask. This is done to avoid 'leaking' of vessels into their neighboring pixels during low-pass.

• Lowpass with the structuring element of defined radius to get F0

• resulting frame = (F-F0)/F0

• Repeat for all frames

The most computationally intensive process is extrapolating of the image into the vessels.