Mahalanobis distance for class averaging of cryo-EM images

Tejal Bhamre, Zhizhen Zhao, Amit Singer

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations


Single particle reconstruction (SPR) from cryo-electron microscopy (EM) is a technique in which the 3D structure of a molecule needs to be determined from its contrast transfer function (CTF) affected, noisy 2D projection images taken at unknown viewing directions. One of the main challenges in cryo-EM is the typically low signal to noise ratio (SNR) of the acquired images. 2D classification of images, followed by class averaging, improves the SNR of the resulting averages, and is used for selecting particles from micrographs and for inspecting the particle images. We introduce a new affinity measure, akin to the Mahalanobis distance, to compare cryo-EM images belonging to different defocus groups. The new similarity measure is employed to detect similar images, thereby leading to an improved algorithm for class averaging. We evaluate the performance of the proposed class averaging procedure on synthetic datasets, obtaining state of the art classification.

Original languageEnglish (US)
Title of host publication2017 IEEE 14th International Symposium on Biomedical Imaging, ISBI 2017
PublisherIEEE Computer Society
Number of pages5
ISBN (Electronic)9781509011711
StatePublished - Jun 15 2017
Event14th IEEE International Symposium on Biomedical Imaging, ISBI 2017 - Melbourne, Australia
Duration: Apr 18 2017Apr 21 2017

Publication series

NameProceedings - International Symposium on Biomedical Imaging
ISSN (Print)1945-7928
ISSN (Electronic)1945-8452


Other14th IEEE International Symposium on Biomedical Imaging, ISBI 2017

All Science Journal Classification (ASJC) codes

  • Radiology Nuclear Medicine and imaging
  • Biomedical Engineering


  • CTF
  • Class averaging
  • Cryo-electron microscopy
  • Denoising
  • Mahalanobis distance
  • Particle picking
  • Single particle reconstruction


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