Appion statistics

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Appion specifications

Information


Unique identifier OMICS_15599
Name Appion
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Database management system MySQL
License Apache License version 2.0
Computer skills Medium
Version 3.3
Stability Stable
Source code URL http://emg.nysbc.org/redmine/projects/appion/files
Maintained Yes

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Maintainer


  • person_outline Gabriel Lander <>

Publications for Appion

Appion in publications

 (98)
PMCID: 5955915
PMID: 29769533
DOI: 10.1038/s41467-018-04272-y

[…] 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 in eman boxer.py via appion. three rounds of reference-free 2d classification were carried out using […]

PMCID: 5905402
PMID: 29617676
DOI: 10.1016/j.celrep.2018.03.027

[…] acquisition software leginon (), and images were acquired on a tietz 4k cmos detector at a magnification of 52,000× and a final pixel size of 2.05 ǻ. raw images were automatically uploaded into the appion database (). particles were individually picked from raw images using dog picker (), placed into a stack, and binned by 2. reference-free two-dimensional classification was done using […]

PMCID: 5830440
PMID: 29491415
DOI: 10.1038/s41467-018-03335-4

[…] grids and stained with 2% uranyl formate. negative stain em images were taken on a 120 kv tecnai spirit microscope with a lab6 filament. raw micrographs were collected using leginon and deposited in appion. dog picker was performed to select particles in stain. those particles were stacked and aligned using iterative msa/mra. 2d classes representing the complex are shown in fig. […]

PMCID: 5823471
PMID: 29425244
DOI: 10.1371/journal.ppat.1006889

[…] image acquisition software package leginon []. the images were acquired at a nominal underfocus of -0.9 μm to -1.8 μm and electron doses of ~25 e-/å2., image processing was performed using the appion software package[]. contrast transfer functions of the images were corrected using ctffind4 []. individual particles in the 67,000× images were selected using automated picking protocols […]

PMCID: 5762779
PMID: 29321502
DOI: 10.1038/s41467-017-02474-4

[…] and a nominal defocus range between 0.5 and 1.5 µm., a total of 1097 micrographs were collected for the complex. initial steps of data processing and 2d analyses were performed using the appion image processing pipeline. the contrast transfer function (ctf) of each micrograph was determined using ctffind v3 implemented within appion. particles were selected from micrographs using […]


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Appion institution(s)
National Resource for Automated Molecular Microscopy, The Scripps Institute, La Jolla, CA, USA; Institute of Molecular Biophysics, Department of Chemistry and Biochemistry, Florida State University, Tallahasse, FL, USA
Appion funding source(s)
This project was primarily funded by grants from the National Institutes of Health (NIH) through the National Center for Research Resources’ P41 program (grants RR17573, RR023093), and additionally by a fellowship from the ARCS foundation.

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