EMPIAR-10464 - SBF SEM images of a Zebrafish hindbrain containing several Toxoplasma gondii tachizoites at different stages of replication [multiple data sets in DM4 format]

EMPIAR-10464

SBF SEM images of a Zebrafish hindbrain containing several Toxoplasma gondii tachizoites at different stages of replication [multiple data sets in DM4 format]

Publication:

The zebrafish as a novel model for the in vivo study of Toxoplasma gondii replication and interaction with macrophages

Yoshida N, Domart MC, Peddie CJ, Yakimovich A, Mazon-Moya MJ, Hawkins TA, Collinson L, Mercer J, Frickel EM, Mostowy S

Disease models & mechanisms 13 (2020)

PMID: 32461265

DOI: 10.1242/dmm.043091

Related EMDB entry:

Deposited:

2020-07-03

Released:

2021-10-27

Last modified:

2022-02-08

Imageset size:

553.92 GB

Imageset DOI:

10.6019/EMPIAR-10464

Experimental metadata:

Download xml json

Contains:

micrographs - single frame

Image Sets

1. Survey SBF SEM images showing the position of the imaged ROIs at the start of each run (3 runs- #20-22)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(None, None)

Details:

Survey images showing the position of the ROIs imaged for each run, if opened in Digital Micrograph.
Variable pixel widths and heights. Run 20: 5000 x 5000, run 21-22: 4096 x 4096. Variable pixel widths. Run 20: 75.6nm, run 21: 87.2nm, run 22: 86.3nm

Files:

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2. Low magnification raw SBF SEM overview images (ROI00) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain over 3 runs (20-22)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

1099

Image size:

(None, None)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(None, None)

Details:

Low magnification overview SBF SEM images (ROI00) for runs 20-22, linked to higher magnification images in ROI01 and ROI02. Imaged at 2kV, 2us dwell, variable pressure 5Pa.
Variable pixel widths and heights. Run 20: 7500 x 5497, run 21: 7000 x 4000, run 22: 6000 x 4000. Variable pixel widths. Run 20: 48.5nm, run 21: 54nm, run 22: 49nm.

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 raw SBF SEM images (ROI01) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain over 3 runs (20-22)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

1099

Image size:

(None, None)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(None, None)

Details:

High magnification images (ROI01) linked to lower magnification images in ROI00, for 3 runs (20-22). Imaged at 2kV, 2us dwell, variable pressure 5Pa.
Variable pixel widths and heights. Run 20: 16384 x 16384, run 21: 15000 x 10000, run 22: 15000 x 12000. Variable pixel widths. Run 20: 6.6nm, run 21-22: 5.8nm.

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 raw SBF SEM images (ROI02) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain (run 20)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

391

Image size:

(8192, 8192)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(69.0, 69.0)

Details:

High magnification images (ROI02) linked to lower magnification images in ROI00 for run 20. Imaged at 2kV, 2us dwell, variable pressure 5Pa.

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 raw SBF SEM images (ROI02) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain for runs 21-22

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

705

Image size:

(None, None)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(None, None)

Details:

High magnification images (ROI02) linked to lower magnification images in ROI00 for run 21-22. Note that it is a different ROI than ROI02-run 20. Imaged at 2kV, 2us dwell, variable pressure 5Pa.
Variable pixel widths and heights. Run 21: 4000 x 4000, run 22: 5000 x 5000. Variable pixel widths. Run 21: 7.1nm, run 22: 6.2nm.

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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