OAD

Microscopy workflow automation toolset

Automating microscopy workflows using Python and Open Application Development tools

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

GitHub

129 stars
19 watching
51 forks
Language: Jupyter Notebook
last commit: about 1 month ago
Linked from 1 awesome list

acquisitionautomationimage-analysisimage-processingimagingmachine-learningmicroscopyoadopen-sourcepythonpython-scriptscriptingworkflowzenzen-blue

Backlinks from these awesome lists:

Related projects:

Repository Description Stars
allencellmodeling/aicsimageio Provides Python tools for reading, writing and managing microscopy images 207
pycroscopy/atomai A PyTorch-based package for analyzing microscopy data with machine learning algorithms 197
ome/openmicroscopy Develops software and data format standards for the storage and manipulation of biological microscopy data. 202
python-microscopy/python-microscopy An application suite for light microscopy acquisition, data storage, visualization, and analysis 85
schmollerlab/cell_acdc A Python framework for analyzing and annotating microscopy data 138
hohlbeinlab/openmicroscopy A collection of resources and projects facilitating collaboration and sharing in the field of microscopy 135
oist/usiigaci Automated cell tracking in phase contrast microscopy images using machine learning and computer vision techniques 193
open-science-tools/nd2reader A software package for reading microscopy images and metadata from NIS Elements files 45
flika-org/flika An interactive image processing tool for analyzing biological microscopy images 22
ziatdinovmax/gpim An open-source Python package for applying Gaussian processes to images and hyperspectral data for reconstruction and Bayesian optimization. 57
fish-quant/big-fish A toolbox for analyzing microscopy images of cells labeled with single-molecule fluorescent in situ hybridization (smFISH) tags. 58
angelolab/ark-analysis A toolset for analyzing multiplexed imaging data by applying various machine learning and image processing techniques to segment cells, cluster pixels, and perform spatial analysis. 78
bmirds/deepslide Classifies high-resolution microscopy images of lung adenocarcinoma using deep neural networks with a sliding window framework. 494
david-hoffman/pyotf Software for simulating optical transfer functions in microscopy using Python 71
jungmannlab/picasso Tools for enhancing image resolution using machine learning algorithms 110