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:

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.

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)

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.

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

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:

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

Quick Links

Talks and Tutorials

EMPIAR Quick tour

Statistics

Publications

Re-use case study

EMPIAR in the news

Claim entries to your ORCiD

COVID-19 Data Portal

EMDB

PDBe

BioImage Archive

EMNavigator@PDBj

PDBj

RCSB@PDBj

EMDataResoruce@RCSB,EMDB,NCMI

Citations

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.

Abe KM, Li G, He Q, Grant T, Lim CJ. (2024)

Outer membrane protein assembly mediated by BAM-SurA complexes.

Fenn KL, Horne JE, Crossley JA, Böhringer N, Horne RJ, Schäberle TF, Calabrese AN, Radford SE, Ranson NA. (2024)

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C. (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)

See all citations

Protein Data Bank Japan News

[2020-07-15]

PDBj는 2020 년 7 월에 20 주년을 맞이했습니다.

[2019-02-20]

[wwPDB] 고분자결정구조 등록 시 PDBx/mmCIF 형식 파일만 허용됩니다.

[2017-11-16]

11 월 24 일 ~ 26 일, 텔레콤 센터 빌딩 (도쿄 오다이바)에서 개최되는 「사이언스 아고라 2017」에 출전합니다

[2016-01-28]

News on 2016-1-11

See all news