EMPIAR-10946 - Processed FIB-SEM images of murine hypothalamus-derived GT1-7 neuronal cells [multiple data sets in TIFF format]

EMPIAR-10946

Processed FIB-SEM images of murine hypothalamus-derived GT1-7 neuronal cells [multiple data sets in TIFF format]

Publication:

Investigating the Role of Spermidine in a Model System of Alzheimer's Disease Using Correlative Microscopy and Super-resolution Techniques

Lumkwana D, Peddie CJ, Kriel J, Michie LL, Heathcote N, Collinson LM, Kinnear C, Loos B

Frontiers in cell and developmental biology (2022)

DOI: 10.3389/fcell.2022.819571

Related EMDB entry:

Deposited:

2022-02-04

Released:

2022-06-22

Last modified:

2022-06-22

Imageset size:

140.48 GB

Imageset DOI:

10.6019/EMPIAR-10946

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. MRC013_EM04295_01_7J_XZ: Control treatment

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

851

Image size:

(5472, 2894)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

MRC013_EM04295_01_7J_XZ: Control treatment

Processed FIB-SEM image series that has been reoriented to the XZ view to match the corresponding SR-SIM dataset (BioStudies B-SST805).

Images were acquired at a nominal isotropic resolution of 5 nm. The SEM was operated at an accelerating voltage of 1.5 kV with 1 nA current. The EsB detector was used with a grid voltage of 1200 V. Ion beam milling was performed at an accelerating voltage of 30 kV and current of 700 pA.

Image processing comprised SIFT registration, denoising (gaussian blur [0.8 pixel radius], smart sharpen [60%, 10 pixel radius, highlights suppressed], smart sharpen [100%, 2 pixel radius, highlight suppressed]), grey level adjustment as required, 8 bit conversion, and rotation and reslice to XZ.

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2. MRC013_EM04295_02_7M_XZ: Bafilomycin treatment

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

921

Image size:

(5907, 5165)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

MRC013_EM04295_02_7M_XZ: Bafilomycin treatment

Processed FIB-SEM image series that has been reoriented to the XZ view to match the corresponding SR-SIM dataset (BioStudies B-SST805).

Images were acquired at a nominal isotropic resolution of 5 nm. The SEM was operated at an accelerating voltage of 1.5 kV with 1 nA current. The EsB detector was used with a grid voltage of 1200 V. Ion beam milling was performed at an accelerating voltage of 30 kV and current of 700 pA.

Image processing comprised SIFT registration, denoising (gaussian blur [0.8 pixel radius], smart sharpen [60%, 10 pixel radius, highlights suppressed], smart sharpen [100%, 2 pixel radius, highlight suppressed]), grey level adjustment as required, 8 bit conversion, and rotation and reslice to XZ.

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. MRC013_EM04295_03_9M_XZ: 1 micromolar spermidine treatment

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

800

Image size:

(5000, 5500)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

MRC013_EM04295_03_9M_XZ: 1 micromolar spermidine treatment

Processed FIB-SEM image series that has been reoriented to the XZ view to match the corresponding SR-SIM dataset (BioStudies B-SST805).

Images were acquired at a nominal isotropic resolution of 5 nm. The SEM was operated at an accelerating voltage of 1.5 kV with 1 nA current. The EsB detector was used with a grid voltage of 1200 V. Ion beam milling was performed at an accelerating voltage of 30 kV and current of 700 pA.

Image processing comprised SIFT registration, denoising (gaussian blur [0.8 pixel radius], smart sharpen [60%, 10 pixel radius, highlights suppressed], smart sharpen [100%, 2 pixel radius, highlight suppressed]), grey level adjustment as required, 8 bit conversion, and rotation and reslice to XZ.

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. MRC013_EM04295_04_8O_XZ: 1 micromolar spermidine / bafilomycin treatment

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1001

Image size:

(5397, 5349)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

MRC013_EM04295_04_8O_XZ: 1 micromolar spermidine / bafilomycin treatment

Processed FIB-SEM image series that has been reoriented to the XZ view to match the corresponding SR-SIM dataset (BioStudies B-SST805).

Images were acquired at a nominal isotropic resolution of 5 nm. The SEM was operated at an accelerating voltage of 1.5 kV with 1 nA current. The EsB detector was used with a grid voltage of 1200 V. Ion beam milling was performed at an accelerating voltage of 30 kV and current of 700 pA.

Image processing comprised SIFT registration, denoising (gaussian blur [0.8 pixel radius], smart sharpen [60%, 10 pixel radius, highlights suppressed], smart sharpen [100%, 2 pixel radius, highlight suppressed]), grey level adjustment as required, 8 bit conversion, and rotation and reslice to XZ.

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. MRC013_EM04295_05_8Q_XZ: 10 micromolar spermidine treatment

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

981

Image size:

(3074, 8420)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

MRC013_EM04295_05_8Q_XZ: 10 micromolar spermidine treatment

Processed FIB-SEM image series that has been reoriented to the XZ view to match the corresponding SR-SIM dataset (BioStudies B-SST805).

Images were acquired at a nominal isotropic resolution of 5 nm. The SEM was operated at an accelerating voltage of 1.5 kV with 1 nA current. The EsB detector was used with a grid voltage of 1200 V. Ion beam milling was performed at an accelerating voltage of 30 kV and current of 700 pA.

Image processing comprised SIFT registration, denoising (gaussian blur [0.8 pixel radius], smart sharpen [60%, 10 pixel radius, highlights suppressed], smart sharpen [100%, 2 pixel radius, highlight suppressed]), grey level adjustment as required, 8 bit conversion, and rotation and reslice to XZ.

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. MRC013_EM04295_06_6K_XZ: 10 micromolar spermidine / bafilomycin treatment

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

900

Image size:

(7052, 5196)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

MRC013_EM04295_06_6K_XZ: 10 micromolar spermidine / bafilomycin treatment

Processed FIB-SEM image series that has been reoriented to the XZ view to match the corresponding SR-SIM dataset (BioStudies B-SST805).

Images were acquired at a nominal isotropic resolution of 5 nm. The SEM was operated at an accelerating voltage of 1.5 kV with 1 nA current. The EsB detector was used with a grid voltage of 1200 V. Ion beam milling was performed at an accelerating voltage of 30 kV and current of 700 pA.

Image processing comprised SIFT registration, denoising (gaussian blur [0.8 pixel radius], smart sharpen [60%, 10 pixel radius, highlights suppressed], smart sharpen [100%, 2 pixel radius, highlight suppressed]), grey level adjustment as required, 8 bit conversion, and rotation and reslice to XZ.

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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Files:

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