pyLattice

A python library for advanced lattice light-sheet image analysis

Welcome!

Installation

clone or download the repository

pip install pylattice
pip install -r requirements.txt
cd src/jupyter
jupyter notebook

in browser open src/jupyter/latticeFrame_showFrame.ipynb

Test data

A small test data set can be found here: https://www.dropbox.com/sh/znznvp1lmvwfykp/AADzJB456aFHll1bYCPzdQhNa?dl=0

Manual

Please read the manual to get started. Read the docs.

Tutorials

Please find tutorials to pyLattice here

FAQ

Lattice Light-Sheet Microscopy

Cite

Please cite our work if you find pyLattice useful: https://doi.org/10.1091/mbc.E18-06-0375

Contribute

Please help us to make LLSM imaging more accessible to the community! Fork the repo, add code and create a pull request. Here you can find our Contributor Guidelines.

References

• scikit http://scikit-image.org
• ChimeraX https://www.cgl.ucsf.edu/chimerax/
• llsm tools https://github.com/francois-a/llsmtools
• utrack https://www.utsouthwestern.edu/labs/danuser/software/#utrack_ancs
• Joh Schöneberg http://www.schoeneberglab.org
• The Betzig Lab https://www.janelia.org/lab/betzig-lab
• The Drubin/Barnes Lab https://drubinbarneslab.berkeley.edu