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ImageJ macro for automated flat-field correction for fluorescence microscopy images and stacks. Effectively a high-pass spatial filter that works better for abnormal backgrounds.
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AutomatedFluorescenceFlatfieldCorrection.ijm
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README.md

README.md

Fluorescence-Flatfield-Correction

ImageJ/FIJI macro for automated flat-field correction for fluorescence microscopy images, timeseries, and stacks. Effectively a high-pass spatial filter that works better for abnormal backgrounds shapes compared to something like a rolling ball filter.


Automated Flatfield Correction Macro

Post-hoc flatfield correction for fluorescence microscopy images. Effectively a lowpass filter. Blurs image with a large gaussian kernel, subtracts blurred image from starting image, adding back the mean of the blurred image to re-establish baseline/bkgd fluorescence.

Intended to be applied to static images, timeseries images, and z-stacks. Not intented for application to multiple color channels. run("Subtract Background...") works better for that.

Generates new image/stack based on most recent selected image/stack.

Copy and paste .ijm file into your 'Macros' folder in your FIJI/ImJ install folder. Open in the macro editor and run, or just load macro and run from the plugins menu.

Written by Wilson Adams, Vanderbilt Biophotonics Center, July 2019

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