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SerialEM specifications


Unique identifier OMICS_15825
Name SerialEM
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format XML
Output format XML
Operating system Windows
Computer skills Medium
Version 3.6
Stability Stable
Source code URL
Maintained Yes




No version available


  • person_outline David Mastronarde <>

Publications for SerialEM

SerialEM citations


Small GTPases and BAR domain proteins regulate branched actin polymerisation for clathrin and dynamin independent endocytosis

PMCID: 5943408
PMID: 29743604
DOI: 10.1038/s41467-018-03955-w

[…] 4k lens coupled ccd camera (direct electron) and a tilt rotate holder (fischione) utilising a tilt range of −60 to +60°. microscope control and image acquisition was accomplished using the software serialem. tilt series were later reconstructed using weighted back projection and fiducial markers (10 nm) into a single volume with imod. to examine areas with the greatest electron density […]


Promotion of virus assembly and organization by the measles virus matrix protein

PMCID: 5928126
PMID: 29712906
DOI: 10.1038/s41467-018-04058-2

[…] nominal magnification) or 6.14 å (10,000× nominal magnification) on the level of the specimen. bidirectional tilt series were semi-automatically collected with 2° angular increments using the serialem package. a cumulative electron dose between 120 and 140 e− å−2 was used. all frames were motion corrected and damage compensated using python scripts ( […]


Isolation of mitochondria from Saccharomyces cerevisiae using magnetic bead affinity purification

PMCID: 5919621
PMID: 29698455
DOI: 10.1371/journal.pone.0196632

[…] at 300 kv, with a gatan k2 summit electron detection (ded) camera (gatan, pleasanton, ca) in super resolution mode. images were then binned down 2x to achieve a pixel size of 2.635 å, using serialem version 3.6 []. tilt series were collected using a bidirectional tilt scheme from 0°±60° with an increment of 1.5° and a defocus range of -5.0 to -6.0 μm. all identified mitochondria […]


Cryo EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins

PMCID: 5933801
PMID: 29684066
DOI: 10.1371/journal.ppat.1007009

[…] were recorded using a gatan k2 summit direct electron detector in the direct electron counting mode (gatan), attached to a fei titan-krios tem, at arizona state university. the automated software serialem [] was used to collect ~2,000 total movies at 37,700x magnification and at a defocus range between 1 and 3 μm. each movie had a total accumulated exposure of 53.66 e/å2 fractionated in 50 […]


Ultrastructural localisation of protein interactions using conditionally stable nanobodies

PMCID: 5903671
PMID: 29621251
DOI: 10.1371/journal.pbio.2005473

[…] ultrathin sections were cut, placed on a slot grid, and imaged on a tecnai 12 transmission electron microscope fitted with a 4k x 4k lc1100 camera (direct electron) at 120 kv under the control of serialem. low-magnification (4,400 xmag) montages were acquired at a binning of 1 and stitched together using the blendmont program in imod. correlation of light and em images was performed using […]


Clathrin adaptor ratio and membrane tension regulate the flat to curved transition of the clathrin coat during endocytosis

PMCID: 5856840
PMID: 29549258
DOI: 10.1038/s41467-018-03533-0

[…] then carefully placed on a glow discharged em grid. samples were dried on filter paper and again imaged with a phase contrast microscope. tem imaging was performed using a jeol 1400 equipped with serialem freeware for montaging. montages of large membrane sheets at 12,000 magnification (1.82 nm per pixel) with 10% overlap were imaged., the fm image and the em montage of the same membrane […]

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SerialEM institution(s)
Boulder Laboratory for Three-Dimensional Electron Microscopy of Cells, Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
SerialEM funding source(s)
This work was supported by NIH/NCRR Grant RR00592 and NIH Program Project Grant P01GM61306.

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