Electron Microscopy Data Analytical Toolkit (EMDA)¶
EMDA is an importable Python library for Electron Microscopy map and model manipulations written in Python3. EMDA comes under MPL-2.0 license.
A selected set of EMDA’s core functionalities include:
Map input/output and format conversion
Resolution related functionalities
Map statistics calculation in Image and Fourier space
Likelihood based map fitting and Bayesian map averaging
Likelihood based magnification refinement
Local correlation map calculation for map and model validation
FSC based map-model validation
To install EMDA, just type following line in the terminal
$ pip install emda
All necessary files will be installed under pythonx.x/site-packages/
To update EMDA, just type
$ pip install -U emda
To test the success of installation, please run the following command in the terminal
All tests will pass, if the installation is successful.
EMDA has several dependencies in addition to general python modules (e.g. Numpy, Scipy). They are Pandas, Gemmi, Mrcfile and Matplotlib. All these dependencies will be automatically checked and installed during EMDA installation.
How to use EMDA¶
There are two ways to access EMDA’s underlying functionalities. EMDA is available as a standalone command line tool to ensure its easy usage. Each functionality is callable with a keyword followed by a set of arguments. Also, EMDA has a simple to use, yet powerful, API for advanced usage documented under emda_methods.
- emda methods module
- emda command line module
- Positional Arguments