Lab News

‘Accidental’ ;-) QTL cloning from our lab published in New Phytologist

A root growth QTL gone astray is a germination QTL:

Amélia Amiguet-Vercher, Luca Santuari, Miguel Gonzalez-Guzman, Stephen Depuydt, Pedro L. Rodriguez and Christian S. Hardtke (2014): The IBO germination QTL encodes a phosphatase 2C-related variant with a non-synonymous amino acid change that interferes with abscisic acid signaling. New Phytologist, doi:10.1111/nph.13225.

Lab News, Video Booth

“Biotechnology & Biodiversity – towards Biotechnoversity?” – now online

Christian’s talk at the Plant Diversity & Seed Heritage event organized by Swissnex San Francisco can now be viewed online. It starts at about 39 min. into the video (chapter 9) and is preceded by a highly educational talk about crop diversity and biotechnology by agricultural scientist Kent Bradford.

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Resources

Code for Sankar et al. 2014

The code for the Automated Quantitative Histology approach described in Sankar, Nieminen & Ragni et al. 2014 is available in the following files that are contained in this linked archive:

IPFactory.py: this file is the pipeline for automated image processing and information extraction.
halfdawn_function.R: this file contains the list of functions for image pre-processing in order to get the binary pictures.
runGetBinarized.R: this file contains the call to the wrapper function *getBinImages* used inside the pipeline.
- postSeg_function.R: this file contains the list of functions for feature extraction and segmentation data processing (color circle map generation, incline angle calculation, etc.)
runGetFeatures.R: this file contains the call to the wrapper function *getFeaturesOverall* used inside the pipeline.
runSaveOverlayedImage.R: this file contains the call to the function *saveOverlayImage* used in the pipeline.
- ML_function.R: this file contains a collection of functions for the machine learning.