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. 2020 Jun 1;36(12):3947-3948.
doi: 10.1093/bioinformatics/btaa218.

PolishEM: image enhancement in FIB-SEM

Jose-Jesus Fernandez  1 , Teobaldo E Torres  2   3 , Eva Martin-Solana  1 , Gerardo F Goya  2   4 , Maria-Rosario Fernandez-Fernandez  1
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PolishEM: image enhancement in FIB-SEM

Jose-Jesus Fernandez et al. Bioinformatics. .

Abstract

Summary: We have developed a software tool to improve the image quality in focused ion beam-scanning electron microscopy (FIB-SEM) stacks: PolishEM. Based on a Gaussian blur model, it automatically estimates and compensates for the blur affecting each individual image. It also includes correction for artifacts commonly arising in FIB-SEM (e.g. curtaining). PolishEM has been optimized for an efficient processing of huge FIB-SEM stacks on standard computers.

Availability and implementation: PolishEM has been developed in C. GPL source code and binaries for Linux, OSX and Windows are available at http://www.cnb.csic.es/%7ejjfernandez/polishem.

Supplementary information: Supplementary data are available at Bioinformatics online.

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