EMPIAR-10473 - Micrograph frames from 110 internal SEMC/NYSBC test datasets used for Topaz-Denoise model generation & analysis [1000000 micrographs in MRCS format]

This entry has been removed from PDBj storage. Please download it from EMPIAR-EBI.

EMPIAR-10473

Micrograph frames from 110 internal SEMC/NYSBC test datasets used for Topaz-Denoise model generation & analysis [1000000 micrographs in MRCS format]

Publication:

Topaz-Denoise: general deep denoising models for cryoEM and cryoET

Bepler T, Kelley K, Noble AJ, Berger B

Nature communications 11 (2020)

PMID: 33060581

DOI: 10.1038/s41467-020-18952-1

Related EMDB entry:

EMD-22052 EMD-22056 EMD-22057 EMD-22058 EMD-22053 EMD-22059 EMD-22060

Deposited:

2019-06-18

Released:

2020-11-27

Last modified:

2021-09-07

Imageset size:

33.93 TB

Imageset DOI:

10.6019/EMPIAR-10473

Experimental metadata:

Download xml json

Contains:

micrographs - single frame

Image Sets

1. Unaligned micrograph frames from 110 internal SEMC/NYSBC test datasets

Category:

micrographs - single frame

Image format:

MRCS

No. of images or tilt series:

1000000

Image size:

(None, None)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(None, None)

Details:

Here are micrograph frames for 110 internal SEMC/NYSBC datasets that we used to generate and analyze numerous different denoising models when writing the Topaz-Denoise software and manuscript. Many of these datasets were used in the pre-trained denoising models included in Topaz. Some frames are in mrcs format, some are in tiff format, and some are zipped with bzip2.

In this EMPIAR entry, you will find an Excel (.xlsx) with sample information, pixelsize, microscope information, and total dose for each dataset.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

Browse All Files

Quick Links

Talks and Tutorials

EMPIAR Quick tour

Statistics

Publications

Re-use case study

EMPIAR in the news

Claim entries to your ORCiD

COVID-19 Data Portal

EMDB

PDBe

BioImage Archive

EMNavigator@PDBj

PDBj

RCSB@PDBj

EMDataResoruce@RCSB,EMDB,NCMI

Citations

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.

Abe KM, Li G, He Q, Grant T, Lim CJ. (2024)

Outer membrane protein assembly mediated by BAM-SurA complexes.

Fenn KL, Horne JE, Crossley JA, Böhringer N, Horne RJ, Schäberle TF, Calabrese AN, Radford SE, Ranson NA. (2024)

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C. (2024)

Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f.

Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. (2024)

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.

Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau VV, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. (2024)

See all citations

Protein Data Bank Japan News

[2024-11-13]

236 new PDB entries have been released on 2024-11-13.

[2024-11-01]

A new portal integrating genome variants and protein structures has released

[2024-10-30]

[wwPDB] Deprecation of FTP File Download Protocol on November 1, 2024

[2024-10-25]

PDBj luncheon seminar at APBJC 2024

[2024-10-17]

[wwPDB] The Nobel Prize in Chemistry 2024