.. pyLattice documentation master file, created by sphinx-quickstart on Fri Jul 27 11:53:40 2018. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. .. http://dont-be-afraid-to-commit.readthedocs.io/en/latest/documentation.html .. http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#rst-primer ************ pyLattice ************ A python library for advanced lattice light-sheet image analysis. Welcome! Visit `pyLattice on Github `_ .. image:: pyLattice_logo.png :width: 1200px :align: center :alt: fig1 Installation ************ clone or download the repository :: pip install pylattice pip install -r requirements.txt cd src/jupyter jupyter notebook You can find the package on `pypi`_. 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. Tutorials ************ Please find tutorials to pyLattice `here`_ FAQ ************ [Lattice Light-Sheet Microscopy](https://en.wikipedia.org/wiki/Lattice_light-sheet_microscopy) Cite ************ Please `cite`_ our work if you find pyLattice useful: - pyLattice: https://doi.org/10.1091/mbc.E18-06-0375 - pyLattice deep_learning: https://doi.org/10.1109/BIBM47256.2019.8983012 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`.: https://docs.google.com/document/d/1Gd5Fr0_sTnez1NEBM7xfisXZ2jR5IbkoLws6EY2Cg2Y/edit?usp=sharing .. _dataset: https://www.dropbox.com/sh/znznvp1lmvwfykp/AADzJB456aFHll1bYCPzdQhNa?dl=0 .. _manual: https://pylattice.readthedocs.io/en/latest/index.html .. _here: https://github.com/JohSchoeneberg/pyLattice_tutorials .. _llsmFAQ: https://en.wikipedia.org/wiki/Lattice_light-sheet_microscopy .. _cite: https://doi.org/10.1091/mbc.E18-06-0375 .. _pypi: https://pypi.org/project/pylattice/ 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 .. toctree:: :maxdepth: 2 :caption: Contents: installation Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`