EMPIAR-11695 - Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network [multiple data sets in TIFF format]

EMPIAR-11695

Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network [multiple data sets in TIFF format]

Publication:

Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network

Lee RG, Rudler DL, Raven SA, Peng L, Chopin A, Moh ESX, McCubbin T, Siira SJ, Fagan SV, DeBono NJ, Stentenbach M, Browne J, Rackham FF, Li J, Simpson KJ, Marcellin E, Packer NH, Reid GE, Padman BS, Rackham O, Filipovska A

Nature cell Biology (---)

Related EMDB entry:

Deposited:

2023-09-18

Released:

2023-10-09

Last modified:

2023-10-09

Imageset size:

434.18 GB

Imageset DOI:

10.6019/EMPIAR-11695

Experimental metadata:

Download xml json

Contains:

micrographs - single frame
micrographs - multiframe
reconstructed volumes

Image Sets

1. Unprocessed FIB-SEM slices acquired from Cal51 wt cells (Sample A)

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

598

Image size:

(6144, 4096)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.372396, 3.372396)

Details:

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

Files:

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2. Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 wt cells (Sample A)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(3002, 909)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

Inputs used to calculate AIVE results for Cal51 wt cells (Sample A), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

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. AIVE outputs generated from FIB-SEM data of Cal51 wt cells (Sample A).

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(3002, 909)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

AIVE outputs generated for FIB-SEM data acquired from Cal51 wt cells (Sample A), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.

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. Unprocessed FIB-SEM slices acquired from Cal51 PEX26ko cells (Sample B)

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

520

Image size:

(6144, 4096)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.372396, 3.372396)

Details:

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

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. Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 PEX26ko cells (Sample B)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(2884, 1075)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

Inputs used to calculate AIVE results for Cal51 PEX26ko cells (Sample B), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

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. AIVE outputs generated from FIB-SEM data of Cal51 PEX26ko cells (Sample B)

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(2884, 1075)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

AIVE outputs generated for FIB-SEM data acquired from Cal51 PEX26ko cells (Sample B), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.

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. Unprocessed FIB-SEM slices acquired from Cal51 GOLGA5ko cells (Sample C)

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

520

Image size:

(6144, 4096)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.372396, 3.372396)

Details:

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

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. Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 GOLGA5ko cells (Sample C)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(2579, 1026)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

Inputs used to calculate AIVE results for Cal51 GOLGA5ko cells (Sample C), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

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. AIVE outputs generated from FIB-SEM data of Cal51 GOLGA5ko cells (Sample C)

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(2579, 1026)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

AIVE outputs generated for FIB-SEM data acquired from Cal51 GOLGA5ko cells (Sample C), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.

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. Unprocessed FIB-SEM slices acquired from Cal51 GOLGA8Mko cells (Sample D)

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

502

Image size:

(6144, 4096)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.372396, 3.372396)

Details:

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

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. Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 GOLGA8Mko cells (Sample D)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(2922, 1158)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

Inputs used to calculate AIVE results for Cal51 GOLGA8Mko cells (Sample D), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

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)

12. AIVE outputs generated from FIB-SEM data of Cal51 GOLGA8Mko cells (Sample D)

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(2922, 1158)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

AIVE outputs generated for FIB-SEM data acquired from Cal51 GOLGA8Mko cells (Sample D), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.

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)

13. Unprocessed FIB-SEM slices acquired from Cal51 SEC61A2ko cells (Sample E)

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

528

Image size:

(6144, 4096)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.372396, 3.372396)

Details:

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

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)

14. Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 SEC61A2ko cells (Sample E)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(3003, 1356)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

Inputs used to calculate AIVE results for Cal51 SEC61A2ko cells (Sample E), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

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)

15. AIVE outputs generated from FIB-SEM data of Cal51 SEC61A2ko cells (Sample E)

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(3003, 1356)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

AIVE outputs generated for FIB-SEM data acquired from Cal51 SEC61A2ko cells (Sample E), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.

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)

16. Unprocessed FIB-SEM slices acquired from Cal51 SEC62ko cells (Sample F)

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

654

Image size:

(6144, 4096)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.372396, 3.372396)

Details:

Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.

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)

17. Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 SEC62ko cells (Sample F)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(2910, 1236)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

Inputs used to calculate AIVE results for Cal51 SEC62ko cells (Sample F), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the "MATTER" & "MEMB" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.

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)

18. AIVE outputs generated from FIB-SEM data of Cal51 SEC62ko cells (Sample F)

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(2910, 1236)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.744792, 6.744792)

Details:

AIVE outputs generated for FIB-SEM data acquired from Cal51 SEC62ko cells (Sample F), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, "Mitos"; Peroxisomes, "Perox"; Endosomes, "EndoCyt & EndoLys"; Endoplasmic reticulum, "ER"; Golgi Apparatus, "Golgi"; Vesicles, "Vesicles"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided ("IndividualFilledMitochondria"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.

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:

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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