Find and compare In Situ expression in Drosophila embryos
Project description
insitu-tools
A set of command line tools that find and compare In situ expression patterns between mRNA expression images, specifically, the Drosophila embryos.
The algorithm used is described in this paper.
Some steps are taken to enhance performance, including:
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Coversion of Color images to grayscale, differentiating stains and embryo texture.
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Linear Transformation of intensity to normalize signals across images.
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4 orientations' comparison to determine the best score.
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Normalize local GMM scores using the self comparison score.
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Global GMM scores (mutual information scores) are calculated on the union area of the 2 embryos.
Installation
pip install seu-insitu-tools
Usages
Detailed descriptions of commands and their arugments are located in our wiki.
Tutorial
Check out the example in our wiki for quick learning of the tools.
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