polishEM

Image enhancement in FIB-SEM (Focused Ion Beam Scanning Electron Microscopy)

J.J. Fernández (1), T. E. Torres (2,3), E. Martín-Solana (1), G. F. Goya (2), M. R. Fernández-Fernández (1)

(1) CINN/CSIC, ISPA. Oviedo. Spain.

(2) Instituto de Nanociencia de Aragón. Universidad de Zaragoza. Spain..

(3) Instituto de Nanociencia y Nanotecnología. Centro Atomico de Bariloche. Argentina.

Contact: jjfernandez.software @ gmail.com

Description

PolishEM is a software tool that enhances FIB-SEM stacks. Based on a Gaussian-blur model, it estimates and compensates for the blur affecting each individual image. This ability provides objectivity in the contrast enhancement and accomodates changes in imaging conditions during the long microscope operation. PolishEM also includes correction for artefacts commonly arising in FIB-SEM (e.g. curtaining). PolishEM has been optimized for an efficient processing of huge FIB-SEM stacks on standard computers, with reduced memory consumption and processing time. PolishEM can work with stacks in MRC and TIF formats. PolishEM can also be applied to other 3DEM modalities (e.g. SBF-SEM).

A detailed description of the procedures implemented in the program can be found in the following article:

PolishEM: image enhancement in FIB-SEM

JJ Fernandez, TE Torres, E Martin-Solana, GF Goya, MR Fernandez-Fernandez

Bioinformatics 36:3947-3948, 2020.

https://doi.org/10.1093/bioinformatics/btaa218

Please, cite this article if you use polishEM in your works.

Download

Current version: November 2019

Available material:

Documentation in PDF: polishEM.pdf
Binaries for 64 bits x86-based platforms under Linux.
Binaries for 64 bits x86-based platforms under Windows 64 bits.
Binaries for 64 bits x86-based platforms under OSX/macOS.

The development of polishEM has been supported by Fundación Ramon Areces and Spanish Ministry of Science.