this repository contains the scripts needed to fit the diameter of diving arterioles as done in Chow, et al. (2019)
sequence of steps to do for tracking:
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crop area of interest and save .tif stack into a new directory make sure the filename contains the bin# and the FOV# as (binX and fovX; case sensitive)
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perform smoothing both spatially and temporally by running 'batchSmoothWrite.m'
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manually set thresholds for each movie by running 'batchThreshold.m' this will save the thresholds in a file called 'manualThresholds.mat' if the manualThresholds file already exists, it will use it instead of asking for inputs it will also write the thresholded movies into the current directory
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move the thresholded images into a new directory
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perform ridge detection on those by running 'medianImageRidgeDetect_batch.ijm' as a batch macro in FIJI
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run fitting using fitDivingArteriole_auto.m in MATLAB to fit all the data
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to export into a spreadsheet, run averageDivingVesselTracking