CTFFIND protocols

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CTFFIND specifications


Unique identifier OMICS_15823
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Fortran
License Other
Computer skills Advanced
Version 4.1
Stability Stable
Maintained Yes


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  • person_outline Nikolaus Grigorieff <>

Publications for CTFFIND

CTFFIND in pipelines

PMCID: 5798934
PMID: 29345620
DOI: 10.7554/eLife.31662.031

[…] was from a total exposure of 2 s dose-fractionated into seven chunks, were collected at a range of underfocus between 0.5 ~ 3 μm. images were motion corrected using motioncorr (), and the program ctffind3 () was used for determining the defocus and astigmatism. images with poor ctf estimation as well as defocus >3 μm were discarded. the spider software package () was used […]

PMCID: 5807052
PMID: 29307485
DOI: 10.1016/j.str.2017.12.003

[…] of 3.5 å at the object scale (a). a semi-automatic particle selection with the eman boxer routine () led to an extraction of a total of ∼68,500 subframes of 80x80 pixels that were ctf-corrected with ctffind3 () and bsoft (), and low-path filtered at 15 å. this data set was subjected to multivariate statistical analysis and classification with imagic-5 (), which led to a removal of ∼11% […]

PMCID: 5807054
PMID: 29395787
DOI: 10.1016/j.str.2017.12.014

[…] the defocus range was 1.3-3.1 μm in 0.3 μm increments; defocus was measured in the autofocus routine every 10 μm., whole-frame alignment was performing using unblur () before ctf estimation using ctffind4 (). all resolution estimates are based on the fsc = 0.143 criterion, and the final resolution estimates were made after the application of a binary mask and phase-randomization to check […]

PMCID: 5834491
PMID: 29500354
DOI: 10.1038/s41467-018-03271-3

[…] processing by visual inspection of the average images and power spectra after the drift correction., the defocus values of the micrographs were measured on the dose-unweighted average images by ctffind4. the dose-weighted average images were used for particle picking and subsequent image processing. a total of 1,729,419 particles were automatically picked using gautomatch [k. zhang, mrc lmb […]

PMCID: 5837792
PMID: 29424687
DOI: 10.7554/eLife.33101.018

[…] of 20 e/a2 at a defocus of between −0.5 and −2.0 μm. particles (15 331) were selected semi-automatically using boxer (). the parameters of the contrast transfer function were then determined with ctffind4 (). particles were 2d-classified into 100 classes in two dimensions using relion () and sixteen well-defined classes were selected for initial three-dimensional reconstruction. initial […]

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CTFFIND in publications

PMCID: 5955915
PMID: 29769533
DOI: 10.1038/s41467-018-04272-y

[…] dose in the em data collection was 32.6 e−/å2. the nominal defocus range used was −1.5 to −3.5 μm., all of the collected frames were aligned prior to processing. ctf estimation was carried out using ctffind3, and particles were picked using an automated particle-picking program implemented in the appion software package. particles were stacked using a box size of 256 × 256 pixels at 1.31 å/pix […]

PMCID: 5928083
PMID: 29712914
DOI: 10.1038/s41467-018-04141-8

[…] particles were picked manually using eman boxer or automatically by template matching in gautomatch (by kai zhang, mrc-lmb cambridge, uk), and the micrograph-based ctf was determined using ctffind4 on drift-corrected, non-dose-weighted images. automatically picked particles were subjected to a first round of reference-free two-dimensional classification with isac within sphire, […]

PMCID: 5916938
PMID: 29695795
DOI: 10.1038/s41467-018-04044-8

[…] of klp10a nm construct in complex with curved tubulin protofilaments in the presence of amp-pnp (supplementary fig. ) were aligned and classified using relion (v 2.0). ctf was estimated using ctffind4. first 10,016 ring-like structures were picked manually from 464 cryo-em images by marking their centers and masking them with a circular mask of 540 å. this set of particles was subjected […]

PMCID: 5908801
PMID: 29674632
DOI: 10.1038/s41467-018-04051-9

[…] complexes by taking the depth of field effect into account (supplementary information). the reconstructions of these simulated images were calculated using the defocus values measured by the program ctffind4 and the known orientation information. the resolution of the reconstructed map was then calculated by comparing the map and the corresponding 3d model using a fsc threshold of 0.5. since […]

PMCID: 5893597
PMID: 29636472
DOI: 10.1038/s41467-018-03785-w

[…] single micrograph that was corrected for overall drift using the motioncor2 program. each drift-corrected micrograph was used for the determination of the actual defocus of the micrograph using the ctffind3 program. reference-free 2d classification was carried out in rome 1.0 that combined the maximum-likelihood-based image alignment and statistical machine-learning-based classification. 3d […]

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CTFFIND institution(s)
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA

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