EMPIAR-12163 - SBF SEM images of a notoroid in longitudinal orientation containing TNE-ZsGreen+ notochord cells (Fig S26 part 2) [multiple data sets in DM4 and TIFF formats]

EMPIAR-12163

SBF SEM images of a notoroid in longitudinal orientation containing TNE-ZsGreen+ notochord cells (Fig S26 part 2) [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

(---)

DOI: 10.1038/s41586-024-08332-w

Related EMDB entry:

Deposited:

2024-03-01

Released:

2024-09-26

Last modified:

2024-09-26

Imageset size:

249.60 GB

Imageset DOI:

10.6019/EMPIAR-12163

Experimental metadata:

Download xml json

Contains:

micrographs - single frame

Image Sets

1. Low magnification raw SBF SEM overview images (ROI02) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run12)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

115

Image size:

(6000, 3994)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(600.0, 600.0)

Details:

Low magnification overview SBF SEM images (ROI02), linked to higher magnification images in ROI03-5 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 (ROI03) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run12)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

115

Image size:

(10000, 8016)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(90.0, 90.0)

Details:

High magnification images (ROI03) linked to lower magnification images in ROI02. 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)

3. Low magnification raw SBF SEM overview images (ROI04) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run12)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

115

Image size:

(10000, 8016)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(90.0, 90.0)

Details:

High magnification images (ROI04) linked to lower magnification images in ROI02. 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 (ROI05) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run12)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

115

Image size:

(10000, 8016)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(90.0, 90.0)

Details:

High magnification images (ROI05) linked to lower magnification images in ROI02 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 (Run13)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

197

Image size:

(6000, 3994)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(600.0, 600.0)

Details:

Low magnification overview SBF SEM images (ROI00), linked to higher magnification images in ROI02 and ROI03 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 (ROI02) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run13)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

197

Image size:

(10000, 8016)

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)

7. Low magnification raw SBF SEM overview images (ROI03) of notoroid with TNE-Zs green notochord in longitudinal orientation (Run13)

Category:

micrographs - single frame

Image format:

DM4

No. of images or tilt series:

197

Image size:

(10000, 5000)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(90.0, 90.0)

Details:

High magnification images (ROI03) 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. 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 12 and 13).

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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