emanuega / storm-analysis Goto Github PK

This is a repository of code developed in the Zhuang lab and the Babcock lab for analysis of STORM movies.

Some algorithms were developed in other groups and ported to Python. In this case the license applies only to our implementation of the code. If you plan to use the algorithm in a commercial product you should discuss this with the original developers (IANAL).

The code should work with both Python2.7 and Python3, but Python3 is recommended.

Discussion Group

The documentation for the latest release is here.

The documentation for git head is here.

Jupyter notebooks that document how to use this project are available in the jupyter_notebooks directory.

Additional notebooks are available here.

Thanks to Google Colaboratory you can install and run storm-analysis on a virtual machine in Google's cloud, no local install necessary. Please see the notebooks in the colab directory here. You will need a Google account to do this.

Docker images are available here.

• FFTW3
• LAPACK

• numpy
• scipy
• matplotlib
• pillow
• tifffile
• Shapely
• randomcolor
• PyWavelets
• PyQt5
• h5py
• astropy

Questions should be addressed to Hazen Babcock (hbabcock at fas.harvard.edu)