cropgeeks/gridscore-next-client

GridScore is a field phenotyping app for trials data.

Language: Vue - Size: 22.4 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 1

Computational-Plant-Science/3D_model_traits_demo

Computation of root phenes from 3D point clouds.

Language: Python - Size: 70.9 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 5 - Forks: 1

mgijax/mammalian-phenotype-ontology

Standard terms for annotating mammalian phenotypic data

Language: Makefile - Size: 648 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 19 - Forks: 6

phytooracle/automation

Modular, Scalable Phenomic Data Processing Pipelines

Language: Python - Size: 1.84 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 4 - Forks: 4

sebastian-raubach/humbug

Humbug is a multi-platform barcode generator which can be used alongside our Germinate Scan application to generate sheets of user-defined barcodes to aid in the recording of data in the field or glasshouse.

Language: Java - Size: 61.9 MB - Last synced: 24 days ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 1

drseb/boqa

Bayesian ontology querying from Bauer et al.

Language: Java - Size: 202 KB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 5 - Forks: 6

robail-yasrab/RootNav-2.0

Plant Phenotyping APP

Language: Python - Size: 22.9 MB - Last synced: 18 days ago - Pushed: about 1 month ago - Stars: 36 - Forks: 18

Asad-Ismail/SMN

Scaleable multitask Network

Language: Python - Size: 61.5 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

akshat22/Field-Book Fork of PhenoApps/Field-Book

Language: Java - Size: 95.9 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

futianfan/PEARL

deep prototype learning for EHR data

Language: Python - Size: 3.52 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 3 - Forks: 0

WGLab/PhenoSV

PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.

Language: Python - Size: 15.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 9 - Forks: 3

obophenotype/human-phenotype-ontology

Ontology for the description of human clinical features

Language: Makefile - Size: 1.54 GB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 278 - Forks: 53

Onto-Med/top-backend

Spring Boot based backend of the TOP Framework

Language: Java - Size: 1.41 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 1

Onto-Med/top-api

REST API of the TOP Framework

Language: Dockerfile - Size: 389 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 1

Computational-Plant-Science/SMART

Monitor and analyze plant growth conditions by computing geometric and color traits from any top-view image dataset

Language: Python - Size: 76.6 MB - Last synced: 19 days ago - Pushed: 3 months ago - Stars: 12 - Forks: 3

Onto-Med/top-deployment

Deployment instructions and resources for the TOP Framework

Language: Smarty - Size: 1.63 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 3

JacobHanimann/scDINO

Self-Supervised Vision Transformers for multiplexed imaging datasets

Language: Python - Size: 19.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 30 - Forks: 8

obophenotype/zebrafish-phenotype-ontology-build

:fish: Zebrafish Phenotype Ontology: Build Tools (OBSOLETE)

Language: Java - Size: 32.8 MB - Last synced: 2 months ago - Pushed: about 6 years ago - Stars: 2 - Forks: 1

EOA-team/sentinel2_crop_traits

Sentinel-2 Crop Trait Retrieval Using Physiological and Phenological Priors from Field Phenotyping (Graf et al., 2023, RSE)

Language: Python - Size: 1.66 GB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 17 - Forks: 4

Daniel-Ze/Leaf-disc-scoring

Leaf disc scoring pipeline for estimating the area of infection on leaf discs from inoculation experiments.

Language: Python - Size: 295 MB - Last synced: 2 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

thsant/3dmcap

3-Demeter Capture is a tool for building 3-D point clouds from images

Language: Python - Size: 5.9 MB - Last synced: 2 months ago - Pushed: over 5 years ago - Stars: 21 - Forks: 3

intervene-EU-H2020/synthetic_data

Software program for generating synthetic datasets for genotypes and phenotypes

Language: Jupyter Notebook - Size: 82.2 MB - Last synced: 2 months ago - Pushed: 12 months ago - Stars: 9 - Forks: 2

Carm1r/phenoclass

Tools for setting objective quantitative levels of expression in phenotypic characterizations

Language: R - Size: 27.3 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

Mmasoud1/HistoJS

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

Language: JavaScript - Size: 290 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 10 - Forks: 0

kclhi/phenoflow

Standardise and share computable disease definitions

Language: JavaScript - Size: 2.72 MB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 7 - Forks: 7

MIAPPE/MIAPPE

Minimum Information About a Plant Phenotyping Experiment

Language: HTML - Size: 4.17 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 21 - Forks: 9

EOA-team/PhenomEn

Repository for the research project "PhenomEn" (Swiss National Science Foundation) - PhD thesis Lukas Valentin Graf

Size: 37.1 KB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

cropandweed/cropandweed-dataset

Information and scripts for the CropAndWeed Dataset

Language: Python - Size: 7.69 MB - Last synced: 4 months ago - Pushed: about 1 year ago - Stars: 38 - Forks: 12

fyz11/SPOT

Generalized and streamlined image phenotyping of dynamic objects over time

Language: Python - Size: 83.3 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

kingrc15/torchmimic

PyTorch library for MIMIC III Benchmark experiments

Language: Python - Size: 187 KB - Last synced: 4 days ago - Pushed: 6 months ago - Stars: 6 - Forks: 1

phenopype/phenopype

A phenotyping pipeline for Python

Language: Python - Size: 23.9 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 9 - Forks: 4

htpmod/HTPmod

an R package for predicting plant biomass accumulation based on image-derived parameters

Language: R - Size: 657 KB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 3 - Forks: 0

jsalojar/PhenomatoR

PhenomatoR: An R Package for the Analysis of Large-Scale Phenomics Data

Language: R - Size: 10.3 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

kevinVervier/CarboLogR

This repository provides a GUI app for phenotype assays analysis from raw data to chemoinformatics.

Language: R - Size: 1.03 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

aafshar/TASTE

Code accompanying our ACM CHIL paper: "TASTE: Temporal and Static Tensor Factorization for Phenotyping Electronic Health Records"

Language: MATLAB - Size: 796 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 7 - Forks: 7

aafshar/COPA

Code accompanying our CIKM paper: "copa: constrained parafac2 for sparse & large datasets"

Language: Matlab - Size: 955 KB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 5 - Forks: 3

andremadsen/Principal_component_analysis

My pipeline for applying PCA for 'endocrine profiling'

Language: R - Size: 9.77 KB - Last synced: 8 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

cbib/linda

Web application for managing experimental and environmental metadata for plant experiments

Language: TypeScript - Size: 31.6 MB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 2 - Forks: 0

Yedomon/Sesame_phenotypic_diversity_analyses

This repository is a compilation of all codes for the phenotypic diversity of a worldwide sesame germplasm from the Korean genebank.

Language: R - Size: 1.79 MB - Last synced: 2 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

wpbonelli/find-ufos

A simple plant tissue segmentation workflow (for Phenome Force 2021)

Language: Python - Size: 3.07 MB - Last synced: 9 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

mchizk1/ShinyFruit

An R shiny app for digital image phenotyping in small fruits

Language: R - Size: 7.74 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 2 - Forks: 1

Computational-Plant-Science/plantit

Language: Vue - Size: 73.1 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 10 - Forks: 3

jeancomp/Plugin

Plugin: application that makes up the OpenDP framework.

Language: Java - Size: 15.3 MB - Last synced: 9 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

NPPC-UK/PAT64V3_W8

The version of PAT64 that Jiwan used to analyse data for the W8 experiment

Language: C++ - Size: 24.4 KB - Last synced: 9 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

openalea/phenotrack3d

Phenotyping Maize over time

Language: Python - Size: 19.5 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 9 - Forks: 2

BenjaminNarhMadey/R-Codes-for-Plant-Breeding-Genetics-Statistics-and-Genomics

This repository serves as a valuable resource for individuals engaged in data exploration, statistical analysis, and research within the domains of plant breeding, genetics, statistics, and genomics. The purpose of this repository is to share a collection of R codes that can be utilized by others for their own data analysis projects

Language: R - Size: 35.2 KB - Last synced: 4 months ago - Pushed: 12 months ago - Stars: 3 - Forks: 0

Computational-Plant-Science/DIRT

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

Language: Python - Size: 998 KB - Last synced: 17 days ago - Pushed: 7 months ago - Stars: 23 - Forks: 15

Computational-Plant-Science/3D_model_reconstruction_demo

Implementation of the 3D reconstruction pipeline optimized for plant branching structures.

Language: C - Size: 84 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 12 - Forks: 2

drseb/HPO-translations

Internationalisation of the HPO content

Size: 11.6 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 20 - Forks: 12

kentavv/flir-batch-process

Batch process FLIR radiometric (thermal) JPEGs and generate clean lossless images with consistent scale and palette

Language: Python - Size: 15.3 MB - Last synced: 10 months ago - Pushed: over 2 years ago - Stars: 5 - Forks: 1

jeffersonfparil/SeedMatic

Seed phenotying and germination assessment using photographs.

Language: Python - Size: 20.3 MB - Last synced: 2 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

cropgeeks/gridscore

GridScore is a field phenotyping app for trials data.

Language: Vue - Size: 9.93 MB - Last synced: 24 days ago - Pushed: 10 months ago - Stars: 2 - Forks: 2

Scan-o-Matic/scanomatic

Scanomatic

Language: Python - Size: 80.7 MB - Last synced: about 1 month ago - Pushed: 8 months ago - Stars: 10 - Forks: 4

fabkury/phea

R package for finding patients in SQL databases using formulas and without using SQL joins

Language: R - Size: 22.1 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 4 - Forks: 0

UTokyo-FieldPhenomics-Lab/EasyDCP Fork of oceam/EasyDCP

A python package for agricultural phenotypic trait extraction from 2D image sets via 3D reconstruction and analysis of 3D point clouds.

Language: Python - Size: 428 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 10 - Forks: 2

ut-biomet/breedSimulatR

R 📦 providing classes and functions to simulate breeding schemes.

Language: R - Size: 4.35 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

picasa/rheliaphen

Tools for phenotyping and modeling with the Heliaphen sunflower phenotyping platform.

Language: R - Size: 23.4 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 2 - Forks: 0

FattaccioliLab/2022-PhenotypingBCellsWithLipidDroplets

Language: R - Size: 1.21 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

PecanProject/bety

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

Language: Ruby - Size: 37.4 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 15 - Forks: 37

jeancomp/OpenDPMH

Framework to Facilitate the Development of Digital Phenotyping Applications

Language: Java - Size: 108 MB - Last synced: 9 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

fishguardians/fishing-on-a-conveyor-belt

Video recording and image analysis of fishes to automate and increase the efficiency of fish phenotyping, and bolster posterior analysis to improve farm production and management.

Language: Python - Size: 62.9 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 2

MrMaximumMax/FBCanalysis

Package to develop and evaluate time series data models based on fluctuation based clustering and Earth Mover's Distances

Language: R - Size: 1.43 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

Computational-Plant-Science/DIRT-storage

Automatic estimation of storage root length, diameter and volume.

Language: Python - Size: 102 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

sauriiiin/sau-matlab-toolkit

Sau's implementation of the MATLAB Colony Analyzer Toolkit and Bean MATLAB Toolkit to analyze high-throughput screening data.

Language: MATLAB - Size: 180 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

sauriiiin/lidetector

LI Detector analytical pipeline for colony-based high-throughput screens.

Language: MATLAB - Size: 82.4 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

openalea/eartrack

An imaging library to detect and track future position of ears on maize plants

Language: Jupyter Notebook - Size: 338 MB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 9 - Forks: 4

germinateplatform/germinate-training

Training material for the use of Germinate

Language: SCSS - Size: 20.5 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

Honghan/KGPhenotyping

knowledge graph based phenotyping

Language: Java - Size: 3.64 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 5 - Forks: 1

van-der-knaap-lab/tomato-analyzer-lite

Extract geometric traits from images of tomatoes, peppers, and more.

Language: Python - Size: 13.2 MB - Last synced: 4 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

callahantiff/PheKnowVec

Translational Computational Phenotyping

Language: Python - Size: 17.7 MB - Last synced: 25 days ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

drseb/HPO-archive

HPO archive of the ontology and annotations

Size: 1.12 GB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 6 - Forks: 2

drseb/phenopposites

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

Size: 19.5 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 3 - Forks: 1

drseb/hpo-obo-qc

The QC software for the OBO version of HPO

Language: Java - Size: 35.2 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

openalea-incubator/rhizoscan

Rhizoscan

Language: Jupyter Notebook - Size: 9.16 MB - Last synced: about 2 months ago - Pushed: almost 5 years ago - Stars: 6 - Forks: 5

robail-yasrab/RSML-to-Image

Language: Python - Size: 6.84 KB - Last synced: 18 days ago - Pushed: almost 4 years ago - Stars: 2 - Forks: 0

robail-yasrab/RootNav-Viewer-2.0

RootNav Viewer 2.0: A visualization tool for Root System Architecture (RSA) using RSML.

Language: C# - Size: 115 KB - Last synced: 18 days ago - Pushed: almost 4 years ago - Stars: 2 - Forks: 0

jasenfinch/pdi

Phenotypic index measures for oak decline severity

Language: R - Size: 762 KB - Last synced: 4 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

Phenomics/phenomics.github.io

Website for the Phenomics and Machine Learning Team

Language: HTML - Size: 2.97 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 3 - Forks: 5

levrex/DeepPhenotypingHPO

Facilitating deep phenotyping by automating the screening of case studies & the comparison of patient similarities (through clustering). This can be used to get an understanding of the underlying pathophysiology for a rare genetic disorder.

Language: HTML - Size: 77.5 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

luoyuanlab/hnmf

Hybrid NMF to integrate genomic data and phenotype data for better patient subtyping. Paper in Bioinformatics.

Language: Matlab - Size: 5.86 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

dschneiderch/WalzPSIIProcessing

A pipeline to process multiframe tifs exported from ImagingWin .pim files

Language: Python - Size: 8.77 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

Onto-Med/phenoman-evaluation

Evaluation of the PhenoMan API with synthetic FHIR data

Language: Shell - Size: 53.7 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

drseb/hpoweb

HPO web browser created with Vaadin

Language: CSS - Size: 1.02 MB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0

drseb/annotation-simulation

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

Language: Java - Size: 3.14 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 2 - Forks: 1

PheMA/phema-population-cql

Simple tool for running a CQL library for a population of patients.

Language: JavaScript - Size: 3.91 KB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

HDRUK/KGPhenotyping Fork of Honghan/KGPhenotyping

knowledge graph based phenotyping

Language: Java - Size: 2.25 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

mocherson/portableNLP

developing a portable NLP-based phenotyping system

Language: Python - Size: 5.96 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 7 - Forks: 1

DryFrost/photogon

Language: C++ - Size: 230 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

surh/RosetteDetector

Rosette Detection with SVM

Language: R - Size: 42.4 MB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0