EMPIAR-12627 - Fib-SEM stacks for Prey (Phaeocystis antarctica) and Host (Ross Sea Dinoflagellate; RSD) [multiple data sets in TIFF format]

EMPIAR-12627

Fib-SEM stacks for Prey (Phaeocystis antarctica) and Host (Ross Sea Dinoflagellate; RSD) [multiple data sets in TIFF format]

Publication:

Hijacking and Integration of Algal Plastids and Mitochondria in a Polar Planktonic Host

Rao AK, Yee D, Chevalier F, Seifi M, Jug F, Deschamps J, Wu TD, Gast R, Jouneau PH, Decelle J, Olivetta M, Dudin O, Gallet B, Hehenberger E

bioRxiv (2024)

DOI: 10.1101/2024.10.20.619283

Related EMDB entry:

Deposited:

2025-03-16

Released:

2025-05-22

Last modified:

2025-05-22

Imageset size:

272.60 GB

Imageset DOI:

10.6019/EMPIAR-12627

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. Aligned Fib-SEM image stacks of 3 different continuously fed RSD Host cells

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

3598

Image size:

(None, None)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(None, None)

Details:

Pixel size for Cell 1 is 6nm with a total of 3598 frames/slices. Cell 2 and Cell 3 are caputred at 5nm resolution with 3280 and 2659 frames respectively. All stacks were aligned and cropped. For segmentation, voxel type was reduced to 8 bits and further binned if necessary (Indicated in supplementary table S3 of the article)

Files:

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2. Aligned Fib-SEM image stacks of 3 different RSD Host cells starved for 9 weeks

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

2244

Image size:

(None, None)

Pixel type:

BIT

Pixel spacing:

(None, None)

Details:

Pixel size for Cell 1, 2 and 3 is 8nm with 695, 1874 and 2244 frames respectively. All stacks were aligned, cropped and converted from 16 bit to 8 bit voxel type. Cell 1 and 3 are inverted. Any binning done during segmentation are indicated in supplementary table S3 of the article

Files:

This entry cannot be downloaded from PDBj.

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. Aligned Fib-SEM image stacks of 5 different prey /Phaeocystis antarctica/ cells in possibly dividing stages

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

755

Image size:

(None, None)

Pixel type:

BIT

Pixel spacing:

(None, None)

Details:

All cells were captured with a 6nm resolution with about 660-755 frames. All stacks were aligned and cropped. Cells 4 and 5 are inverted and converted to 8 bit voxel type while cells 1-3 remain as 16 bit voxel type.
For segmentation, voxel type for all cells was reduced to 8 bits

Files:

This entry cannot be downloaded from PDBj.

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. Aligned Fib-SEM image stacks of 7 different prey /Phaeocystis antarctica/ cells

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

688

Image size:

(None, None)

Pixel type:

BIT

Pixel spacing:

(None, None)

Details:

All cells were captured with a 6nm resolution with about 462-688 frames. All stacks were aligned and cropped. Cells 4-7 are inverted and converted to 8 bit voxel type while cells 1-3 remain as 16 bit voxel type.
For segmentation, voxel type was reduced to 8 bits for all cells

Files:

This entry cannot be downloaded from PDBj.

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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