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Automatic phenotyping tool for 3D images

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LAMA (Lightweight Analysis of Morphological Abnormalities)

Welcome to LAMA, an open source pipeline to automatically identify embryo dysmorphology from 3D volumetric images.

It was originally developed for use with whole-embryo ct scans of knockout mice coming from the International Mice Phenotyping Consortium (http://www.mousephenotype.org), but has been shown to work with other data types such as HREM.

Getting Started

See the lama wiki And the interactive walkthroughs

Built With

  • Python3
  • elastix - For image registration
  • R - Statistics
  • Scipy - Image analysis
  • SimeITK - Image IO and analysis

Authors

This software was developed by Neil Horner in the Bioimage Informatics Group at MRC Harwell UK (https://www.har.mrc.ac.uk) under the supervision of Henrik Westerberg.

If you have any questions or comments, please contact us at [email protected]

License

This project is licensed under the Apache License, Version 2.0 - see the LICENSE.md file for details

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