EMPIAR-11666 - Benchmark SBF SEM data of HeLa cells previously imaged by Zeiss LSM900 Airyscan microscopy [multiple data sets in DM4 and TIFF formats]

EMPIAR-11666

Benchmark SBF SEM data of HeLa cells previously imaged by Zeiss LSM900 Airyscan microscopy [multiple data sets in DM4 and TIFF formats]

Publication:

CLEM-Reg: An automated point cloud based registration algorithm for correlative light and volume electron microscopy

Krentzel D, Elphick M, Domart M, Peddie CJ, Laine RF, Henriques R, Collinson LM, Jones ML

bioRxiv (2023)

DOI: 10.1101/2023.05.11.540445

Related EMDB entry:

Deposited:

2023-08-22

Released:

2023-09-05

Last modified:

2023-09-05

Imageset size:

39.16 GB

Imageset DOI:

10.6019/EMPIAR-11666

Experimental metadata:

Download xml json

Contains:

micrographs - single frame
micrographs - multiframe

Image Sets

1. Low magnification raw SBF SEM overview images (ROI00) of the region around the cell imaged in ROI01

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

138

Image size:

(2000, 2000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(752.916, 752.916)

Details:

SBF SEM images from a Gatan 3View on a Zeiss Sigma SEM. Low magnification consecutive overview images (ROI00) linked to higher magnification images in ROI01. 50nm thick slices. Imaged at 2kV with a 20um aperture, 2us dwell, 65% then 70% FCC after slice 26.

Files:

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2. Low magnification raw SBF SEM overview images (ROI00) of HeLa cell previously imaged by Airyscan

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

138

Image size:

(9000, 9000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(70.148, 70.148)

Details:

SBF SEM images from a Gatan 3View on a Zeiss Sigma SEM. High magnification images (ROI01) linked to lower magnification images in ROI00. 50nm thick slices. Imaged at 2kV with a 20um aperture, 2us dwell, 65% then 70% FCC after slice 26.

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. High magnification aligned full resolution SBF SEM image stack

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(10717, 9845)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(70.148, 70.148)

Details:

Processed and aligned (in TrakEM2) tif stack of SBF SEM images of HEla cell at full resolution (7nm XY, 50nm Z) with similar orientation to the Airyscan data available on Biostudies

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. High magnification aligned downscaled to 14nm XY SBF SEM image stack

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(5359, 4923)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(140.296, 140.296)

Details:

Processed and aligned tif stack of SBF SEM images downscaled (14nm XY, 50nm Z) with similar orientation to the Airyscan data available on Biostudies

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)

5. High magnification aligned downscaled to 28nm XY SBF SEM image stack

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(2679, 2461)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(280.593, 280.593)

Details:

Processed and aligned tif stack of SBF SEM images downscaled 28nm XY, 50nm Z) with similar orientation to the Airyscan data available on Biostudies

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:

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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.

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