SARA: SIMA And RAIN Analysis

Demonstrates use of SIMA to analyze a TIFF stack of a confocal microscopy imaging session.

The following files make for a complete example: sara.py, SARA.ipynb, and original.tif

Limitations

Currently I only support single-channel imaging.

Prerequisites: What you need to use SARA

1. A solid understanding of programming with Python (especially if you will be using serial.py)
2. The SIMA 1.0 module must be installed on your computer
3. One or more single-channel confocal microscopy video recordings stored as TIFF stacks.

Analyzing multiple recordings

serial.py is an example showing how to run several analysis jobs automatically. It is NOT intended to be used without first understanding it and modifying it to work with your own system (e.g. if you use a computing cluster).