SerialEM protocols

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SerialEM specifications

Information


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 http://bio3d.colorado.edu/ftp/SerialEM/
Maintained Yes

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Maintainer


  • person_outline David Mastronarde <>

Publications for SerialEM

SerialEM in pipelines

 (31)
2018
PMCID: 5758107
PMID: 29249608
DOI: 10.1016/j.str.2017.11.011

[…] data was recorded on either a tf30, tf30 polara or titan krios microscope (fei), equipped with k2 direct electron detectors and quantum energy filters (gatan). tomographic data was collected with serialem () or fei tomography, with pixel sizes between 2 and 3 å/pixel at the specimen level and the energy selecting slit set to 20 ev, with a collection scheme of ±45° tilts (starting from 0° up, […]

2018
PMCID: 5823459
PMID: 29470533
DOI: 10.1371/journal.ppat.1006837

[…] was done using fei tecnai f20 microscope operated at 200kv and equipped with gatan ultrascan 4k x 4k ccd camera. the random comical tilt (rct) image pairs were acquired semi-automatically using serialem 3.6.3 [] at nominal magnification of 50,000x with pixel size of 2.18a and defocus of 1.2–1.8 μm. the tilt pair was collected at -60° and 0°., to generated 3d model of the rsv f-fab complexes […]

2017
PMCID: 5218534
PMID: 28059701
DOI: 10.7554/eLife.20070.021

[…] by negative staining with 0.75% (w/v) uranyl formate (). data were collected with a tecnai f20 (fei) equipped with a schottky field emission gun and operated at an acceleration voltage of 120 kv. serialem () was used for automatic data collection using low-dose procedures at a calibrated magnification of 88,000× and a defocus value of −2.0 μm. images were recorded on a 4k × 4k ccd tietz […]

2017
PMCID: 5345008
PMID: 28281671
DOI: 10.1038/srep44176

[…] filter (slit width: 20 ev). condenser and objective apertures were set at 50 and 60 μm respectively. the specimens were kept at −170 °c with liquid nitrogen. tilt series images were collected using serialem automated data acquisition software in a range of ±62° at 2° increments. the images were recorded on a 4k × 4k pixels slow scan ccd camera (gatan inc.) at a nominal magnification of × 20 k, […]

2017
PMCID: 5655142
PMID: 29035201
DOI: 10.7554/eLife.31054.029

[…] data was collected on a titan krios 300 kv cryo-electron microscope (fei) in the multi-scale microscopy core at oregon health and science university, assisted by the automated acquisition program serialem. images were recorded on the gatan k2 summit direct electron detector in super-resolution mode, post-gif (20 ev window), at the nominal magnification 81,000x (calibrated image pixel-size […]


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SerialEM in publications

 (250)
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 […]

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 (de_process_frames-2.8.1.py […]

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 […]

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 […]

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 […]


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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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