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This is a convenient code wrapper to run Lundberg lab SubCell model in inference with your own images
MultiCell: geometric learning in multicellular development
A Python package for feature extraction of neural morphologies
A library of free open source icons for science illustrations in biology and chemistry
A framework for distributed large-scale image registration
Because setting up bio image analysis tools shouldn’t cost you your sanity
Next generation FEniCS Form Compiler for finite element forms
NL‑BIOMERO delivers a full containerized stack to run OMERO together with the BIOMERO 2.0 framework. It provides Docker/Podman configurations and Compose files to deploy OMERO + BIOMERO subsystems …
This repo is a list of papers that discuss errors in research due to software errors
Data Inspection Plugin, designed to streamline file navigation and enhance the efficiency of data inspection.
A simple automated feedback microscopy tool for live tracking of moving samples.
BISCUIT (BioImage Segmentation Comparison Utility and Interactive Tool) is an open-source platform for visually comparing state-of-the-art cell segmentation models on microscopy data. Run models in…
Rust extension module for FIJI-like colormapping and channel blending
Interactive image stack viewing in jupyter notebooks based on ipycanvas and ipywidgets
Retrieve author and publication information from Google Scholar in a friendly, Pythonic way without having to worry about CAPTCHAs!
An introduction to OME-Zarr for big bioimaging data
Qualitative evaluation of OME-NGFF readers/writers at the Next generation bioimage analysis workflows hackathon 2023 in Zurich, Switzerland
A fully scalable robust image feature extraction library.
Python code associated to "Fast volumetric fluorescence lifetime imaging of multicellular systems using single-objective light-sheet microscopy" by Dunsing-Eichenauer, Hummert et al., bioRxiv 2024.…
Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.
Python API for functional imaging in neuroscience