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FISH-FINDER: Version 4 David McSwiggen, Dec 2016

This script uses gaussian detection/localization as applied by the SLIMfast implementation of MTT in order to detect spots coming from a maximum projection image of FISH data in multiple colors. Then it will attempt to pair up spots from the different images in order to determine colocalization.

To effectively use this code, one should have images in a .TIFF format, and have at least two separate FISH color channels as well as DAPI (or similar) to allow for the segmentation of cells. Filepaths to each image should be provided, and the code can take into account different replicates uding the "Position_number" and "Replicate_number" variables.

After detection of all spots, a threshold must be used to determine which are truly mRNA and which are background noise. This threshold will depend on the parameters used to aquire the images, and may be very different from those used in the Chen, Tresenrider, et. al. manuscript.

For more information, or to address specific questions, please email or direct them to the corresponding authors of the Chen, Tresenrider, et. al. manuscript.

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