cisTEM protocols

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chevron_left 3D macromolecule reconstruction CTF estimation/correction Image registration Image classification Particle picking Single particle analysis chevron_right
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cisTEM specifications


Unique identifier OMICS_26527
Name cisTEM
Alternative name Computational Imaging System for Transmission Electron Microscopy
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Version 1.0.0
Stability Beta
Source code URL
High performance computing Yes
Maintained Yes



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Publication for Computational Imaging System for Transmission Electron Microscopy

cisTEM in pipeline

PMCID: 5458492
PMID: 28580912
DOI: 10.1107/S2059798317004181

[…] are trying to redress the imbalance with new and improved solutions; for instance, jeol with a new automatic specimen-loading system, a redesigned frealign with a graphical user interface (cistem; personal communication with timothy grant, janelia research campus), and the fei falcon iii camera, which will even be retrofitted onto the most recently sold fei microscope systems […]

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cisTEM in publications

PMCID: 5655137
PMID: 29027901
DOI: 10.7554/eLife.28560.031

[…] contamination, or very thin ice were excluded from further analysis after inspection of image sums and power spectra from ctffind4. particles were automatically picked from full-sized images using cistem, software that implements a template-based algorithm (). 560 × 560 pixel boxes with particles were extracted from super-resolution images, and the stack and frealign parameter file […]

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

[…] reported shortly after we submitted our paper. to address this, we had already started reprocessing the data using relion version 2.1b1 upon its release. in addition, we were also starting to use cistem (frealign) to further improve the maps via 3d classification and improved masking of the micelle. this combination resulted in a map that was almost the same, though slightly improved, […]

PMCID: 4436252
PMID: 25992920
DOI: 10.1371/journal.pone.0127055

[…] neighbouring stems from the effects of larger stems. furthermore, as a more complex measure of competition, we calculated the tree-level density-dependent hegyi competition index [] for both stems (cistem) and trees (citree), also within a radius of 12 m around each stem or tree. the formula of the hegyi competition index is as follows: cihegyi=∑j=1ndjdi(lij+1) where di is the dbh of subject […]

PMCID: 2361608
PMID: 16136028
DOI: 10.1038/sj.bjc.6602740

[…] patient no. 007, who was not evaluable for toxicity. patients experiencing thrombocytopenia grade 0–2 had higher levels of mgmt at baseline (median 14.5 fm μg−1, range 3.1–52.5 fm μg−1) and after cistem treatment (median 5.5 fm μg−1, range 0.6–31.3 fm μg−1) than patients with grade 3 toxicity (median 6.7 fm μg−1, range 2.8–15.9 fm μg−1 at baseline; p=0.0158; and median 2.2 fm μg−1, range […]

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