FISH v1

Disclaimer:
This package contains files from the FieldTrip project to compute the intersection between a line and a mesh.

How to use:
These files add 3 options in a "FISH" submenu in the "Image processing" menu of Imaris:

• The first script will attempt to create a 3D model of your image.
• The second script will regenerate the statistics (useful if the objects are modified).
• The last script will export the statistics to a "FISH" folder in "public documents" (Windows).

By using "FISH > 3D Model", Imaris will attempt to create a 3D model of the image, with surfaces (nuclei) and spots. It will also create a new channel containing an index for each nucleus. Finally, it will compute new statistics for each spot:

• Distance from the nucleus centroid to the spot
• Distance from the nucleus centroid to the border of the nucleus, through the spot

Using "FISH > Regenerate the stats" will compute the statistics again.

Finally, "FISH > Export the stats" will create a csv file with the results in "Public Documents\FISH".

Installation:
Place the content of the zip file in your custom Imaris XT folder.