https://github.com/Computational-Plant-Science/DIRT

Digital Imaging of Root Traits: Extract trait measurements from images of monocot and dicot roots.

computer-vis image-processing imaging phenotyping phenotyping-algorithms root

Last synced: 07 May 2025

https://github.com/drseb/hpo-translations

Internationalisation of the HPO content

hpo hpo-translations language obofoundry ontology phenomics phenotype-ontologies phenotypes phenotyping semantic-web translation

Last synced: 09 Apr 2025

https://github.com/mmasoud1/histojs

HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

cell-cell-interaction cell-segmentation digital-slide-archive image-processing mibiscope multichannel multiplexed-imaging multiplexed-imaging-analysis ome-tiff phenotyping proteomics proteomics-data-analysis single-cell spatial-biology spatial-data-analysis whole-slide-imaging

Last synced: 16 May 2025

https://github.com/PecanProject/bety

Web-interface to the Biofuel Ecophysiological Traits and Yields Database (used by PEcAn and TERRA REF)

agriculture crops database ecosystem-models pecan phenotyping plants postgis ruby trait

Last synced: 07 May 2025

https://github.com/Computational-Plant-Science/plantit

hpc phenomics phenotyping science-gateways singularity

Last synced: 08 May 2025

https://github.com/drseb/hpo-archive

HPO archive of the ontology and annotations

annotations archive hpo hpo-archive ontology phenomics phenotype-ontologies phenotypes phenotyping

Last synced: 09 Apr 2025

https://github.com/drseb/boqa

Bayesian ontology querying from Bauer et al.

bayesian-inference hpo obofoundry phenotype phenotype-ontologies phenotypes phenotyping similarity

Last synced: 14 Feb 2025

https://github.com/lewis-stuart-11/3d-plant-view-synthesis

Main repo for the running/training on the dataset presented in 'High-fidelity Wheat Plant Reconstruction using 3D Gaussian Splatting and Neural Radiance Fields'

3d computer-vision dataset gaussian-splatting machine-learning neural-radiance-fields phenotyping plant-growth plant-phenotypes plant-phenotyping plants view-synthesis wheat

Last synced: 02 Apr 2025

https://github.com/drseb/phenopposites

Project to generate phenotype opposite_of relationships and investigate the effect on ontology-based algorithms

ontologies ontology phenomics phenotype phenotype-ontologies phenotypes phenotyping semantic-web semantics similarity-measures

Last synced: 09 Apr 2025

https://github.com/interpretamr/amrgen

The AMRgen package provides tools for interpreting antimicrobial resistance (AMR) genes, integrating genomic data with phenotypic antimicrobial susceptibility testing (AST) data, and calculating genotype-phenotype associations.

eucast genotyping phenotyping r

Last synced: 02 Jan 2025

https://github.com/callahantiff/pheknowvec

Translational Computational Phenotyping

abra-collaboratory computational-phenotyping omop open-biomedical-ontologies phenotyping

Last synced: 09 Apr 2025

https://github.com/drseb/annotation-simulation

Code to generate ontology annotated objects (e.g. HPO annotated patients)

hpo hpo-annotated-patients patients phenotype phenotype-ontologies phenotypes phenotyping simulation

Last synced: 09 Apr 2025

https://github.com/asad-ismail/smn

Scaleable multitask Network

deep-learning image-processing instance-segmentation keypoint-detection multitask-learning phenomics phenotyping pytorch vegetable

Last synced: 13 May 2025

https://github.com/drseb/hpoweb

HPO web browser created with Vaadin

browser hpo ontologies ontology phenomics phenotype-ontologies phenotypes phenotyping website

Last synced: 09 Apr 2025

https://github.com/wpbonelli/find-ufos

image segmentation workflow for Phenome Force 2021

boundary-detection computer-vision image-segmentation phenome phenotyping

Last synced: 05 May 2025

https://github.com/drseb/hpo-obo-qc

The QC software for the OBO version of HPO

hpo obofoundry ontology phenomics phenotype phenotype-ontologies phenotypes phenotyping quality-control

Last synced: 09 Apr 2025

https://github.com/jasenfinch/pdi

Phenotypic index measures for oak decline severity

decline index oak phenotyping r

Last synced: 29 Mar 2025