Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

navigate - open source light-sheet microscope controls

Control, reconstruction, and analysis code for oblique plane microscopy.

Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.

#ZVQ - Zebrafish Vascular Quantification - https://doi.org/10.1242/dev.199720

shrimPy: Smart High-throughput Robust Imaging & Measurement in Python

MATLAB tools for handling mesoSPIM data

Lazy loader napari plugin for mesoSPIM datasets

A integrated analysis toolbox for 3D spatial transcriptome, enables highly accurate 3D registration for large volume images, and provides barcoding and decoding analysis for spatial transcriptome of thick tissue.

MAXWELL: A tandem use X-ray/visible light microscopy technique at BL29XU of the RIKEN SPring-8 Center, Japan.

Image acquisition software for mesoSPIM light-sheet microscopes.