EMPIAR-12041 - FIB-SEM datasets of hippocampal neurons from WT and FAM92A1 knockout mice [multiple data sets in TIFF format]

EMPIAR-12041

FIB-SEM datasets of hippocampal neurons from WT and FAM92A1 knockout mice [multiple data sets in TIFF format]

Publication:

Membrane remodeling by FAM92A1 during brain development regulates neuronal morphology, synaptic function, and cognition

Wang L, Yang Z, Satoshi F, Prasanna X, Yan Z, Vihinen H, Chen Y, Zhao Y, He X, Bu Q, Li H, Zhao Y, Jiang L, Qin F, Dai Y, Zhang N, Qin M, Kuang W, Zhao Y, Jokitalo E, Vattulainen I, Kajander T, Zhao H, Cen X

Nature communications 15 (2024)

PMID: 39043703

DOI: 10.1038/s41467-024-50565-w

Related EMDB entry:

Deposited:

2023-12-22

Released:

2024-12-02

Last modified:

2024-12-02

Imageset size:

73.62 GB

Imageset DOI:

10.6019/EMPIAR-12041

Experimental metadata:

Download xml json

Contains:

micrographs - single frame

Image Sets

1. FIB-SEM dataset of WT mouse hippocampal neurons (DG region)

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

1950

Image size:

(2205, 592)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

FIB milling step 5 nm. Images were acquired with pixel size 2.5 nm, xy binned by 2 resulting in voxel size 5x5x5 nm.
The SEM (Zeiss Crossbeam 540) was operated at an accelerating voltage of 1.4 kV with 0.3 nA current. The ESB detector was used with a grid voltage of 1000 V. Ion beam milling was performed at an accelerating voltage of 30 kV and current of 700 pA.
Images were aligned, grey level adjusted and converted to 8 bit using Zeiss Atlas 5 software.

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2. FIB-SEM dataset of hippocampal neurons (DG region) from FAM92A1 KO mouse

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

894

Image size:

(5143, 816)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

FIB milling step 5 nm. Images were acquired with pixel size 2.5 nm, xy binned by 2 resulting in voxel size 5x5x5 nm.
The SEM (Zeiss Crossbeam 540) was operated at an accelerating voltage of 1.4 kV with 0.3 nA current. The EsB detector was used with a grid voltage of 1000 V. Ion beam milling was performed at an accelerating voltage of 30 kV and current of 700 pA.
Images were aligned, grey level adjusted and converted to 8 bit using Zeiss Atlas 5 software.

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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rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

3. raw FIB-SEM dataset of WT mouse hippocampal neurons (DG region)

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

1999

Image size:

(8768, 8768)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(25.0, 25.0)

Details:

Raw images from WT-1 sample (10.10.2022) acquired with Zeiss crossbeam 540. Images were acquired with pixel size 2.5 nm, milling thickness 5 nm. The SEM was operated at an accelerating voltage of 1.4 kV with 0.3 nA current. The ESB detector was used with a grid voltage of 1000 V. Ion beam milling was performed at an accelerating voltage of 30 kV and current of 700 pA. Both ESB and Inlens images were collected.

Files:

This entry cannot be downloaded from PDBj.

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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. raw FIB-SEM dataset of hippocampal neurons (DG region) from FAM92A1 KO mouse

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

903

Image size:

(14976, 14976)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(25.0, 25.0)

Details:

Raw images from HO-1 sample (10.10.2022) acquired with Zeiss crossbeam 540. Images were acquired with pixel size 2.5 nm, milling thickness 5 nm. The SEM was operated at an accelerating voltage of 1.4 kV with 0.3 nA current. The ESB detector was used with a grid voltage of 1000 V. Ion beam milling was performed at an accelerating voltage of 30 kV and current of 700 pA. Both ESB and Inlens images were collected.

Files:

This entry cannot be downloaded from PDBj.

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We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

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