ILE is a software package for segmentation, localization, post-processing and visualization of 2D single molecule localization microscopy (SMLM) data. The package includes post-processing routines for combining signals occuring in consecutive frames, filtering and drift correction. As visualization routines it includes the following methods: scatterplot, histogram binning, Gaussian blurring, triangulation, Voronoi tesselation and local density-based visualization. ILE provides a GUI and allows batch processing. For a quick overview take a look at ILE's workflow.
The following sections describe how to install a copy of the software. Detailed instructions can be found in the manual.
-
Matlab R2012a or newer
- Statistics and Machine Learning Toolbox
- Image Processing Toolbox
-
multiWaitbar (a copy is included in this distribution)
- download the software package from https://github.com/Jan-NM/ILE
- extract ILE-master.zip
- copy the generated ILE-master directory into your local Matlab working directory (on Windows machines, usually C:\Users\ "user name"\Documents\MATLAB)
- to use ILE, right click on ILE-master in Matlab's current folder panel, go to "Add to Path" and click on "Selected Folders and Subfolders"
- type "startSPDM" in the command window. Detailed instructions on how to use the software can be found in the manual.
ILE is licensed under the GNU GPL - see the LICENSE file for details. ILE includes multiWaitbar, which comes with a separate license.
ILE's segmentation and localization algortihm is based on: Grüll at al., "Accelerating Image Analysis for Localization Microscopy with FPGAs", (2011).
This project is forked from: https://gitlab.com/microscopy/ILE