Protomo statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left 3D image reconstruction Tomogram and subtomogram averaging chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

Protomo specifications

Information


Unique identifier OMICS_27805
Name Protomo
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Shell (Bash)
License GNU General Public License version 3.0
Computer skills Medium
Version 2.4.2
Stability Stable
Registration required Yes
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Hanspeter Winkler <>

Additional information


http://www.electrontomography.org/?page_id=317

Publication for Protomo

Protomo in pipelines

 (3)
2014
PMCID: 3916419
PMID: 24516628
DOI: 10.1371/journal.pone.0088288

[…] for tilt series with fiducial markers, tomographic alignment and reconstruction was performed using imod software . tilt series without fiducial markers were aligned and reconstruction using protomo software . in this method, alignment of the original projection images is iterated until relative image shifts are less than 1 pixel and geometrical correction factors are within 1%. […]

2014
PMCID: 3949170
PMID: 24487619
DOI: 10.1038/nature12951

[…] biology center. images were acquired with a 4096 x 4096 ccd camera and binned by a factor of 2 at 8.85 nm pixel size. image alignment and tomographic reconstructions were obtained using the protomo software package. fiducial-free single axis tomograms were combined using imod and tomogram segmentation performed using the amira software package. models were constructed and rendered […]

2011
PMCID: 3239172
PMID: 21919528
DOI: 10.1021/cr100353t

[…] subtomogram averaging., automation is indispensable for electron tomography.() well-developed tomography software is available from both academic and commercial sources (serialem;() ucsf tomo;() protomo;() tom;() xplore3d;() imod,). leginon incorporates tomographic and other tilt data collection protocols such as conical tilt ().(), although theoretical and technical progress in electron […]


To access a full list of citations, you will need to upgrade to our premium service.

Protomo in publications

 (7)
PMCID: 5660141
PMID: 28733815
DOI: 10.1007/s10974-017-9477-5

[…] or other structural z-disk proteins, or due to excessive radiation damage., the tilt series were aligned using marker-free alignment and the tomogram computed by weighted back projection using the protomo software package (winkler and taylor ). generally, protomo uses a cross correlation between the tilt series image and a reference calculated by reprojecting a preliminary back projection […]

PMCID: 4813320
PMID: 26801085
DOI: 10.1242/jcs.181743

[…] software (jeol, usa inc, peabody, ma). the tilt range was approximately −60 to +60 degrees, using a nominal 2-degree interval with cosine adjustment. tomogram reconstruction was performed using the protomo software package ()., j774 cells were incubated with colloidal-gold-labeled agldl for 1 h (). after incubation with agldl the cells were fixed with a modified karnovsky's solution containing […]

PMCID: 4762132
PMID: 26942219
DOI: 10.1007/s41048-015-0009-9

[…] 1.02 nm/pixel. the dose for each tilted image was about 1 e/å2, and the defocus was set to 3 μm. in total, 25 sets of tomographic data were collected. they were then aligned and reconstructed with protomo software package. median filtering was applied to the reconstructed tomograms to enhance the signal-to-noise ratio. matlab was used for the power spectrum analysis., the imaging […]

PMCID: 4336559
PMID: 24809274
DOI: 10.1111/cmi.12310

[…] microscope (fei) equipped with 1k × 1k ccd camera (gatan) at a nominal magnification of 23 000 (corresponding to a pixel size of 0.83 nm). fiducial-free alignment of tilt images was carried out in protomo (winkler and taylor, ), and the two reconstructions from the dual-axis tilt series were merged in imod (kremer et al., ; mastronarde, ). the final reconstructions were median-filtered (3 × 3) […]

PMCID: 3916419
PMID: 24516628
DOI: 10.1371/journal.pone.0088288

[…] for tilt series with fiducial markers, tomographic alignment and reconstruction was performed using imod software . tilt series without fiducial markers were aligned and reconstruction using protomo software . in this method, alignment of the original projection images is iterated until relative image shifts are less than 1 pixel and geometrical correction factors are within 1%. […]


To access a full list of publications, you will need to upgrade to our premium service.

Protomo institution(s)
Florida State University, Institute of Molecular Biophysics, Tallahassee, FL, USA
Protomo funding source(s)
Supported by NIH Grant GM30598 and Grant GM64346 to the Cell Migration Consortium.

Protomo reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Protomo