Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes

Streamline your ecoacoustic analysis with LEAVES, offering advanced tools for large-scale soundscape annotation and visualization. Join researchers and citizen scientists using LEAVES to analyze complex soundscapes faster and more accurately.

Fungal Validation and Identification Pipeline

BirdNET as a systemd service with other features.

Raspir, the rare species identifier

banter is a package for creating hierarchical acoustic event classifiers out of multiple call type detectors.

MitoSIS (Mitochondrial Species Identification System) is a wrapper for mitochondrial genome assembly and identification of sample contamination or mislabeling.

Naturblick iOS

Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies

This repository contains code for preprocessing, training, evaluation, and inferencing of two models, SSD and Faster R-CNN, for the task of bird detection and classification. For details about the Flask web application built on this model visit the link below.

Image classification pipeline for natural sciences

A Flask web application for the classification of bird species built using TFServing, Docker and MySQL.

Species Identification and Prediction by Mass Spectrometry

Tree seedling detection and species identification using YOLO + BioCLIP

Parser of BLAST results

GUI app to manage imagery from a (bird) feeder camera, including species classification, sorting images into folders and export to Observation.org-compatible CSV. Processing is fully local, but the app allows uploading manual labels and automatically checks for updates.

Species identification based on mass spectrometry biomarker clustering

Tools for manipulating the Wildlife Watcher, a smart camera to monitor animals in the wild.

Docker images for the SpeciesNet networks.

DNA barcoding analysis pipeline