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LAMA

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 originating from the International Mice Phenotyping Consortium (http://www.mousephenotype.org), but has been shown to work with other data types such as HREM.

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]

User documentation

See the following sections for instructions on how to use LAMA

• Getting started
• Data preprocessing
• Lama workflow
• Registration
• Make a population average
• Generate baseline and mutant data
• label propagation
• Stats pipeline
• QC
• Utilities
• Interactive walkthroughs