phenotyping

There are 5 repositories under phenotyping topic.

human-phenotype-ontology
obophenotype / human-phenotype-ontology
Ontology for the description of human clinical features
hpo ontology phenotype phenotyping ontologies obo owl semantic-web obofoundry monarchinitiative
Language:Makefile 278
cropandweed / cropandweed-dataset
Information and scripts for the CropAndWeed Dataset
agriculture dataset detection crop weed classification segmentation farming phenotyping plants computer-vision object-detection plant-monitoring semantic-segmentation crop-classification weed-detection benchmark deep-learning crops weeds
Language:Python 56
robail-yasrab / RootNav-2.0
Plant Phenotyping APP
rootnav python plant phenotyping plant-monitoring plant-growth machine-learning deep-learning artificial-intelligence rootnav2 root-phenotyping plant-phenotyping plant-phenotypes
Language:Python 36
JacobHanimann / scDINO
Self-Supervised Vision Transformers for multiplexed imaging datasets
high-content-screening self-supervised-learning single-cell fluorescence-microscopy-imaging greyscale-image morphology multi-channel multi-head-attention phenotyping vision-transformer unsupervised
Language:Python 30
Computational-Plant-Science / DIRT
Digital Imaging of Root Traits: Extract trait measurements from images of monocot and dicot roots.
phenotyping phenotyping-algorithms root imaging image-processing computer-vis
Language:Python 23
MIAPPE / MIAPPE
Minimum Information About a Plant Phenotyping Experiment
metadata data-management phenotyping plant-sciences research
Language:HTML 22
thsant / 3dmcap
3-Demeter Capture is a tool for building 3-D point clouds from images
3-dimension computer-vision phenotyping point-cloud
Language:Python 22
drseb / HPO-translations
Internationalisation of the HPO content
translation language ontology semantic-web hpo hpo-translations phenomics phenotypes phenotyping phenotype-ontologies obofoundry
20
mgijax / mammalian-phenotype-ontology
Standard terms for annotating mammalian phenotypic data
obofoundry phenotyping ontology phenotype owl obo json mammals
Language:Makefile 19
EOA-team / sentinel2_crop_traits
Sentinel-2 Crop Trait Retrieval Using Physiological and Phenological Priors from Field Phenotyping (Graf et al., 2023, RSE)
chlorophyll leaf-area-index phenology phenotyping physiology remote-sensing sentinel-2
Language:Python 17
HistoJS
Mmasoud1 / HistoJS
HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
cell-cell-interaction cell-segmentation mibiscope multiplexed-imaging multiplexed-imaging-analysis ome-tiff phenotyping proteomics proteomics-data-analysis single-cell whole-slide-imaging digital-slide-archive image-processing multichannel spatial-biology spatial-data-analysis
Language:JavaScript 15
PecanProject / bety
Web-interface to the Biofuel Ecophysiological Traits and Yields Database (used by PEcAn and TERRA REF)
pecan ruby trait database postgis agriculture plants phenotyping crops ecosystem-models
Language:Ruby 15
Computational-Plant-Science / 3D_model_reconstruction_demo
Implementation of the 3D reconstruction pipeline optimized for plant branching structures.
phenotyping phenotyping-algorithms root
Language:C 14
Computational-Plant-Science / SMART
Monitor and analyze plant growth conditions by computing geometric and color traits from any top-view image dataset
phenotyping computer-vision image-segmentation extract-traits artificial-intelligence-algorithms u-net-pytorch
Language:Python 12
UTokyo-FieldPhenomics-Lab / EasyDCP
A python package for agricultural phenotypic trait extraction from 2D image sets via 3D reconstruction and analysis of 3D point clouds.
phenotyping
Language:Python 12
plantit
Computational-Plant-Science / plantit
hpc science-gateways phenotyping phenomics singularity
Language:Vue 10
intervene-EU-H2020 / synthetic_data
Software program for generating synthetic datasets for genotypes and phenotypes
bioinformatics data-generator generative-model genetics genomics julia phenotypes phenotyping polygenic-risk-scores polygenic-scores simulation synthetic-data
Language:Jupyter Notebook 10
Scan-o-Matic / scanomatic
Scanomatic
python bioinformatics biology image-processing flask phenotyping science
Language:Python 10
openalea / eartrack
An imaging library to detect and track future position of ears on maize plants
maize image-processing openalea phenotyping python
Language:Jupyter Notebook 9
openalea / phenotrack3d
Phenotyping Maize over time
maize openalea organs phenotyping tracking
Language:Python 9
phenopype / phenopype
A phenotyping pipeline for Python
computer-vision image-analysis image-processing phenotyping biology-images ecology evolution phenomics
Language:Python 9
WGLab / PhenoSV
PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.
phenotyping structural-variants transformer variant-interpretation
Language:Python 9
aafshar / TASTE
Code accompanying our ACM CHIL paper: "TASTE: Temporal and Static Tensor Factorization for Phenotyping Electronic Health Records"
tensor healthcare predictive-modeling phenotyping unsupervised-learning electronic-health-record ehr-phenotyping
Language:MATLAB 7
drseb / HPO-archive
HPO archive of the ontology and annotations
hpo annotations hpo-archive ontology archive phenomics phenotypes phenotyping phenotype-ontologies
7
kclhi / phenoflow
Standardise and share computable disease definitions
phenomics common-workflow-language phenotyping
Language:JavaScript 7
kentavv / flir-batch-process
Batch process FLIR radiometric (thermal) JPEGs and generate clean lossless images with consistent scale and palette
python flir flir-cameras thermography phenotyping plant-phenotyping
Language:Python 7
mocherson / portableNLP
developing a portable NLP-based phenotyping system
nlp phenotyping
Language:Python 7
aafshar / COPA
Code accompanying our CIKM paper: "copa: constrained parafac2 for sparse & large datasets"
tensor tensor-factorization tensor-decomposition parafac2 matlab healthcare phenotyping
Language:MATLAB 6
kingrc15 / torchmimic
PyTorch library for MIMIC III Benchmark experiments
clinical decompensation in-hospital-mortality length-of-stay mimic-iii phenotyping pytorch
Language:Python 6
openalea-incubator / rhizoscan
Rhizoscan
openalea root rsa phenotyping
Language:Jupyter Notebook 6
Computational-Plant-Science / 3D_model_traits_demo
Computation of root phenes from 3D point clouds.
phenotyping phenotyping-algorithms phenomics root
Language:Python 5
drseb / boqa
Bayesian ontology querying from Bauer et al.
hpo phenotype similarity bayesian-inference phenotypes phenotyping phenotype-ontologies obofoundry
Language:Java 5
fabkury / phea
R package for finding patients in SQL databases using formulas and without using SQL joins
omop-cdm phenotyping
Language:R 5
Honghan / KGPhenotyping
knowledge graph based phenotyping
reusable phenotyping health-data
Language:Java 5
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
breeding genomics-analysis genomics-visualization phenotyping plant statistics
Language:R 4
phytooracle / automation
Modular, Scalable Phenomic Data Processing Pipelines
hpc makeflow phenomics phenotyping pipeline plant python workqueue distributed-computing lettuce plant-phenotyping sorghum
Language:Python 4

phenotyping

obophenotype / human-phenotype-ontology

cropandweed / cropandweed-dataset

robail-yasrab / RootNav-2.0

JacobHanimann / scDINO

Computational-Plant-Science / DIRT

MIAPPE / MIAPPE

thsant / 3dmcap

drseb / HPO-translations

mgijax / mammalian-phenotype-ontology

EOA-team / sentinel2_crop_traits

Mmasoud1 / HistoJS

PecanProject / bety

Computational-Plant-Science / 3D_model_reconstruction_demo

Computational-Plant-Science / SMART

UTokyo-FieldPhenomics-Lab / EasyDCP

Computational-Plant-Science / plantit

intervene-EU-H2020 / synthetic_data

Scan-o-Matic / scanomatic

openalea / eartrack

openalea / phenotrack3d

phenopype / phenopype

WGLab / PhenoSV

aafshar / TASTE

drseb / HPO-archive

kclhi / phenoflow

kentavv / flir-batch-process

mocherson / portableNLP

aafshar / COPA

kingrc15 / torchmimic

openalea-incubator / rhizoscan

Computational-Plant-Science / 3D_model_traits_demo

drseb / boqa

fabkury / phea

Honghan / KGPhenotyping

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

phytooracle / automation