pyLattice¶
A python library for advanced lattice light-sheet image analysis.
Welcome!
Visit pyLattice on Github
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
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
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
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
Matlab on Macs¶
If matlab throws errors like this:
Invalid MEX-file
'/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice/src/matlab/trackingModule/dependencies/u-track/software/mex/createDistanceMatrix.mexmaci64':
dlopen(/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice/src/matlab/trackingModule/dependencies/u-track/software/mex/createDistanceMatrix.mexmaci64,
6): Library not loaded: @loader_path/libmex.dylib
Referenced from:
/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice/src/matlab/trackingModule/dependencies/u-track/software/mex/createDistanceMatrix.mexmaci64
Reason: image not found.
The solution can be found here:
https://stackoverflow.com/questions/48458660/library-not-loaded-loader-path-libmex-dylib-in-matlab
First, find out your matlab version:
find /Applications/ -maxdepth 1 -type d -name 'MAT*'
In my case this is:
MATLAB_R2017b.app
In the subsequent steps, the 2017b matlab version is used. If you have a different version, replace MATLAB_R2017b.app with your version below.
You have to add the libraries to your matlab startup script:
/Applications/MATLAB_R2017b.app/bin/.matlab7rc.sh.
Add:
DYLD_LIBRARY_PATH="/Applications/MATLAB_R2017b.app/bin/maci64:/Applications/MATLAB_R2017b.app/sys/os/maci64"
Then startup matlab from the command line:
/Applications/MATLAB_R2017b.app/bin/matlab