Post Processing

There are several options for post processing of output images and files. The two most common are to load the saved data into matlab, or to load images into ImageJ (or Fiji) and perform processing using built in features of this software.

Matlab post-processing

ImageJ (Fiji) post-processing

Loading .sc files into ImageJ is straightforward. Select File->Import->Raw... and the dialog below should appear. The image type should be 32-bit Real for .sc files and the width and height will vary depending on the camera. The Offset to first image will always be 6 bytes for .sc files. Make sure Little-endian byte order is checked as well.

Once the image(s) are loaded, common analysis steps include:

• adjustment of the display range using Image->Adjust->Window Level. Sometimes it’s easiest to select a region in the image and click Auto in the Window Level dialog.
• colormaps can be applied to the image through Image->Lookup Tables
• average values within regions can be obtained by selecting a region, then using Analyze->Measure

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