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.

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]

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