EMPIAR-12162 - SBF SEM images of a notoroid in longitudinal orientation containing TNE-ZsGreen+ notochord cells (Fig S26 part 1) [multiple data sets in DM4 and TIFF formats]

EMPIAR-12162

SBF SEM images of a notoroid in longitudinal orientation containing TNE-ZsGreen+ notochord cells (Fig S26 part 1) [multiple data sets in DM4 and TIFF formats]

Publication:

Notochord and axial progenitor generation by timely BMP and NODAL inhibition during vertebrate trunk formation

Tiago Rito TR, Ashley R.G. Libby ARGL, Madeleine Demuth MD, Marie-Charlotte Domart MCD, Jake Cornwall-Scoones JCS, James Briscoe JB

(---)

Related EMDB entry:

Deposited:

2024-03-01

Released:

2024-09-26

Last modified:

2024-09-26

Imageset size:

169.97 GB

Imageset DOI:

10.6019/EMPIAR-12162

Experimental metadata:

Download xml json

Contains:

micrographs - single frame

Image Sets

1. Low magnification raw SBF SEM overview images (ROI00) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run02)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

Image size:

(7000, 12000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(590.0, 590.0)

Details:

Low magnification overview SBF SEM images (ROI00), linked to higher magnification images in ROI01 and ROI02 below. Imaged at 1.8kV, 2us dwell, with a 20um aperture and with FCC. 50nm slices.

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2. High magnification raw SBF SEM overview images (ROI01) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run02)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

Image size:

(12000, 12000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(90.0, 90.0)

Details:

High magnification images (ROI01) linked to lower magnification images in ROI00. Imaged at 1.8kV, 2us dwell, with a 20um aperture and with FCC. 50nm slices.

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.

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3. Low magnification raw SBF SEM overview images (ROI00) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run03)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

Image size:

(6000, 3000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(800.0, 800.0)

Details:

Low magnification overview SBF SEM images (ROI00), linked to higher magnification images in ROI01 below. Imaged at 1.8kV, 2us dwell, with a 20um aperture and with FCC. 50nm slices.

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.

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4. High magnification raw SBF SEM overview images (ROI01) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run03)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

Image size:

(12000, 5932)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(90.0, 90.0)

Details:

High magnification images (ROI01) linked to lower magnification images in ROI00 Imaged at 1.8kV, 2us dwell, with a 20um aperture and with FCC. 50nm slices.

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. Low magnification raw SBF SEM overview images (ROI00) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run04)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

168

Image size:

(6000, 3000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(800.0, 800.0)

Details:

Low magnification overview SBF SEM images (ROI00), linked to higher magnification images in ROI01 and ROI02 below. Imaged at 1.8kV, 2us dwell, with a 20um aperture and with FCC. 50nm slices.

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 overview images (ROI01) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run04)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

168

Image size:

(12000, 5932)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(90.0, 90.0)

Details:

High magnification images (ROI01) linked to lower magnification images in ROI00 Imaged at 1.8kV, 2us dwell, with a 20um aperture and with FCC. 50nm slices.

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 raw SBF SEM overview images (ROI02) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run04)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

168

Image size:

(8000, 5932)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(90.0, 90.0)

Details:

High magnification images (ROI02) linked to lower magnification images in ROI00 Imaged at 1.8kV, 2us dwell, with a 20um aperture and with FCC. 50nm slices.

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. Low magnification raw SBF SEM overview images (ROI00) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run06)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

Image size:

(6000, 3000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(800.0, 800.0)

Details:

Low magnification overview SBF SEM images (ROI00), linked to higher magnification images in ROI01 and ROI02 below. Imaged at 1.8kV, 2us dwell, with a 20um aperture and with FCC. 50nm slices.

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)

9. High magnification raw SBF SEM overview images (ROI01) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run06)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

Image size:

(8000, 6010)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(90.0, 90.0)

Details:

High magnification images (ROI01) linked to lower magnification images in ROI00 Imaged at 1.8kV, 2us dwell, with a 20um aperture and with FCC. 50nm slices.

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)

10. High magnification raw SBF SEM overview images (ROI02) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run06)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

Image size:

(8000, 6010)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(90.0, 90.0)

Details:

High magnification images (ROI02) linked to lower magnification images in ROI00 Imaged at 1.8kV, 2us dwell, with a 20um aperture and with FCC. 50nm slices.

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)

11. Survey images

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

Survey images showing the relative position of the ROIs for each Run (Run 2, 3, 4 and 6).

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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