EMPIAR-10463 - SBF SEM images of a Zebrafish hindbrain containing several Toxoplasma gondii tachizoites at different stages of replication [multiple data sets in DM4 and TIFF formats]

EMPIAR-10463

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

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:

2020-12-09

Last modified:

2022-02-08

Imageset size:

175.17 GB

Imageset DOI:

10.6019/EMPIAR-10463

Experimental metadata:

Download xml json

Contains:

micrographs - single frame
micrographs - multiframe

Image Sets

1. Survey SBF SEM image showing the position of the 5 imaged ROIs at the start of the run

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

Image size:

(5000, 5000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(742.5, 742.5)

Details:

Survey image showing the position of the 5 ROIs imaged (ROI00, 01-4) if opened in Digital Micrograph

Files:

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2. Low magnification raw SBF SEM overview images (ROI00) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

354

Image size:

(6500, 5000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(504.0, 504.0)

Details:

Low magnification overview images (ROI00) linked to higher magnification images in ROI01. Imaged at 2kV, 2us dwell, variable pressure 5Pa.

Files:

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

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3. High magnification raw SBF SEM images (ROI01) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

354

Image size:

(15000, 8000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(60.0, 60.0)

Details:

High magnification images (ROI01) linked to lower magnification images in ROI00. 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)

4. High magnification raw SBF SEM images (ROI02) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

354

Image size:

(8000, 8000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(64.0, 64.0)

Details:

High magnification images (ROI02) linked to lower magnification images in ROI00. 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 (ROI03) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

354

Image size:

(4000, 8000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(64.0, 64.0)

Details:

High magnification images (ROI03) linked to lower magnification images in ROI00. 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)

6. High magnification raw SBF SEM images (ROI04) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

354

Image size:

(3000, 3000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(78.0, 78.0)

Details:

High magnification images (ROI04) linked to lower magnification images in ROI00. 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)

7. Low magnification aligned SBF SEM images (ROI00) with segmentation of middle section of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

354

Image size:

(3025, 2326)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(500.0, 500.0)

Details:

Low magnification aligned (least square in TrakEM2) overview SBF SEM images (ROI00) and manual segmentation (channel 2) of middle sections of Toxoplasma tachizoites. Used for correlation with fish 1 (see Biostudies link). See Fig 2 of the paper.

Files:

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Browse All Files

Files:

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