Biological Image Analysis
144 items from hallvaaw/awesome-biological-image-analysis ★198
-
TrackMate github.com
User-friendly interface that allows for performing tracking, data visualization, editing results and track analysis in a convenient way.
-
-
-
AICSImageIO github.com
Image reading, metadata conversion, and image writing for nicroscopy images in Python.
-
CellSAM github.com
A foundation model for cell segmentation trained on a diverse range of cells and data types.
-
Ultrack github.com
Versatile cell tracking method for 2D, 3D, and multichannel timelapses, overcoming segmentation challenges in complex tissues.
-
Usiigaci github.com
Stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning.
-
PyTorch Connectomics github.com
Deep learning framework for automatic and semi-automatic annotation of connectomics datasets, powered by PyTorch.
-
Cell-ACDC github.com
A GUI-based Python framework for segmentation, tracking, cell cycle annotations and quantification of microscopy data.
-
CaPTk github.com
Cancer Imaging Phenomics Toolkit: A software platform to perform image analysis and predictive modeling tasks.
-
-
BG-atlasAPI github.com
A lightweight Python module to interact with atlases for systems neuroscience.
-
-
OAD github.com
Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools.
-
CellProfiler Analyst github.com
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
-
-
-
-
Spotiflow github.com
A deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method developed for spatial transcriptomics workflows.
-
-
-
PlantSeg github.com
Tool for cell instance aware segmentation in densely packed 3D volumetric images.
-
-
-
Trainable Weka Segmentation github.com
Fiji plugin and library that combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations.
-
FlashDeconv github.com
High-performance spatial transcriptomics deconvolution (~1M spots in ~3 min).
-
ThunderSTORM github.com
A comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging.
-
-
PYME github.com
Open-source application suite for light microscopy acquisition, data storage, visualization, and analysis.
-
Nellie github.com
Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy.
-
Wholebrain github.com
Automated cell detection and registration of whole-brain images with plot of cell counts per region and Hemishpere.
-
Pyotf github.com
A simulation software package for modelling optical transfer functions (OTF)/point spread functions (PSF) of optical microscopes written in Python.
-
-
-
NeuroAnatomy Toolbox github.com
R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
-
-
-
-
-
MAPS github.com
MAPS (Machine learning for Analysis of Proteomics in Spatial biology) is a machine learning approach facilitating rapid and precise cell type identification with human-level accuracy from spatial proteomics data.
-
-
Minerva github.com
Image viewer designed specifically to make it easy for non-expert users to interact with complex tissue images.
-
-
RS-FISH github.com
Fiji plugin to detect FISH spots in 2D/3D images which scales to very large images.
-
-
Aradeepopsis github.com
A versatile, fully open-source pipeline to extract phenotypic measurements from plant images.
-
-
-
ZetaStitcher github.com
Tool designed to stitch large volumetric images such as those produced by light-sheet fluorescence microscopes.
-
- next page of items loading…
