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This repository contains some of the image processing tools we use in the Raj Lab primarily to analyze single molecule RNA-FISH data.

Getting Started

We have written out step by step installation instructions and a worked example using data bundled with the installation.

Getting the latest version

Once you've installed rajlabimagetools, to get the latest version, navigate to your installation directory in the terminal and run:

$ git pull https://github.com/arjunrajlaboratory/rajlabimagetools.git

Documentation

• Installation instructions

• Worked example

• 3D spot visualizer

• Data structure and low-level tools

• Defining custom data and image processing steps

• Batch processing tools

• Bundled GUIs

• SNP FISH

• SNP FISH 3D spot viewer

• Two color colocalization

• Two color colocalization 3D spot viewer

• Transcription Sites Analysis

• Expansion Microscopy + RNA FISH (ExFISH) Worked Example

• Blob Analyzer

• Semi-manual measurement of distance from transcription site to speckle

• Calculate total fluorescence intensity

Compatibility

If you created image objects with the version of rajlabimagetools existing prior to May 15th, 2014, they used a different underlying data structure. Go to the compatibility repository and follow the instructions to convert any saved data that uses the older image object.

RNA Spot Finding in Tiled Images

rajlabimagetools contains a sub-package devoted to analyzing tiled images for RNA spots. See its documentation.

License

We have not figured this out yet. Please assume for now no right to distribute copies or modifications of this software. Point them here instead.

Contributors

The image tools have been an effort in the Rajlab since even before it formally existed.

People who have made major contributions (thousands of lines of code) to past and present versions of the code:

• Arjun Raj

• Marshall Levesque

• Gautham Nair

• Matthew MacLean

• Paul Ginart

Code from external sources:

The handy function dlmcell.m written by Roland Pfister is included here but was originally obtained from the matlab file exchange at:

#!html

http://www.mathworks.com/matlabcentral/fileexchange/25387-write-cell-array-to-text-file/content/dlmcell.m