EMPIAR-10819 - Benchmark FIB SEM data of HeLa cells previously imaged by Zeiss LSM900 Airyscan microscopy [multiple data sets in TIFF format]

EMPIAR-10819

Benchmark FIB SEM data of HeLa cells previously imaged by Zeiss LSM900 Airyscan microscopy [multiple data sets in TIFF format]

Publication:

Raw and processed benchmark FIB SEM data matching Airyscan data deposited on Biostudies

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

(---)

Related EMDB entry:

Deposited:

2020-08-14

Released:

2021-10-29

Last modified:

2021-10-29

Imageset size:

1.68 TB

Imageset DOI:

10.6019/EMPIAR-10819

Experimental metadata:

Download xml json

Contains:

micrographs - single frame
micrographs - multiframe

Image Sets

1. Raw FIB SEM run 1 part 1

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

1599

Image size:

(12032, 12032)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(50.0, 50.0)

Details:

First part of the raw data (out of 4 in total).
Images were acquired at 5 nm isotropic resolution throughout the region of interest, using a 6 us dwell time. During acquisition the SEM was operated at an accelerating voltage of 1.5 kV with 1.5 nA current.

Files:

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2. Raw FIB SEM run 1 part 2

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

1600

Image size:

(12032, 12032)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(50.0, 50.0)

Details:

Second part of the raw data (out of 4 in total).
Images were acquired at 5 nm isotropic resolution throughout the region of interest, using a 6 us dwell time. During acquisition the SEM was operated at an accelerating voltage of 1.5 kV with 1.5 nA current.

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. Raw FIB SEM run 1 part 3

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

1534

Image size:

(12032, 12032)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(50.0, 50.0)

Details:

Third part of the raw data (out of 4 in total).
Images were acquired at 5 nm isotropic resolution throughout the region of interest, using a 6 us dwell time. During acquisition the SEM was operated at an accelerating voltage of 1.5 kV with 1.5 nA current.

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. Raw FIB SEM run 2

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

1261

Image size:

(12032, 12032)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(50.0, 50.0)

Details:

Last part of the raw data (out of 4 in total).
Images were acquired at 5 nm isotropic resolution throughout the region of interest, using a 6 us dwell time. During acquisition the SEM was operated at an accelerating voltage of 1.5 kV with 1.5 nA current.

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. Aligned full resolution FIB SEM stack in its original orientation

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(7000, 965)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

Processed and aligned stack of FIB SEM images at 5 nm isotropic resolution in the original orientation of the acquisition

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)

6. Aligned full resolution FIB SEM stack resliced to match the orientation of the Airyscan data

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(5938, 7000)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

Processed and aligned stack of FIB SEM images at 5 nm isotropic resolution resliced to match the orientation of the Airyscan data available on Biostudies S-BSST707

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)

7. Downscaled (10nm) aligned FIB SEM stack resliced to match the Airyscan dataset

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(2969, 3500)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(100.0, 100.0)

Details:

Processed and aligned stack of FIB SEM images downscaled to 10 nm isotropic resolution and resliced to match the orientation of the Airyscan data available on Biostudies S-BSST707

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)

8. Downscaled (20nm) aligned FIB SEM stack resliced to match the Airyscan dataset

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(1485, 1750)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(200.0, 200.0)

Details:

Processed and aligned stack of FIB SEM images downscaled to 20 nm isotropic resolution and resliced to match the orientation of the Airyscan data available on Biostudies S-BSST707

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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