EMPIAR-11841 - Automatically collected tilt series on cryoFIB milled lamellae of Baker's Yeast [multiple data sets in TIFF and MRC formats]

EMPIAR-11841

Automatically collected tilt series on cryoFIB milled lamellae of Baker's Yeast [multiple data sets in TIFF and MRC formats]

Publication:

Smart Parallel Automated Cryo Electron tomography

Eisenstein F, Fukuda Y, Danev R

bioRxiv (2023)

Related EMDB entry:

EMD-38295

Deposited:

2023-12-12

Released:

2024-07-03

Last modified:

2024-07-03

Imageset size:

1.20 TB

Imageset DOI:

10.6019/EMPIAR-11841

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame
stitched maps
tilt series

Image Sets

1. Unaligned frames for all tilts of all tilt series of Yeast lamellae using SPACEtomo

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(4092, 5760)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(2.09, 2.09)

Details:

camera orientation: rotation by 90, flipped around y axis

Files:

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.

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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)

2. Projections of reconstructed tomograms using AreTomo2

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(510, 720)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(16.72, 16.72)

Details:

Automatically XY projections from AreTomo2 reconstructions of all tomograms for screening tilt series content.

Files:

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

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)

3. Montages of lamellae and grids collected by SPACEtomo

Category:

stitched maps

Image format:

MRC

No. of images or tilt series:

Image size:

(4092, 5760)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(18.9, 18.9)

Details:

Montages of lamellae of varying sizes and full grids collected automatically by SPACEtomo

Files:

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

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)

4. Meta information in form of mdoc files for all tilt series

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(2.09, 2.09)

Details:

All mdoc files (unsorted) without dose information. Dose was 4.35 e/A^2/tilt.

Files:

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

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

Files:

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

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)

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Citations

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

CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM.

Fan X, Zhang Q, Zhang H, Zhu J, Ju L, Shi Z, Hu M, Bao C. (2024)

Self-assembled superstructure alleviates air-water interface effect in cryo-EM.

Zheng L, Xu J, Wang W, Gao X, Zhao C, Guo W, Sun L, Cheng H, Meng F, Chen B, Sun W, Jia X, Zhou X, Wu K, Liu Z, Ding F, Liu N, Wang HW, Peng H. (2024)

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