EMPIAR-12885 - Source data for AI-directed voxel extraction and volume EM identify intrusions as sites of mitochondrial contact [multiple data sets in TIFF format]

EMPIAR-12885

Source data for AI-directed voxel extraction and volume EM identify intrusions as sites of mitochondrial contact [multiple data sets in TIFF format]

Publication:

AI-directed voxel extraction and volume EM identify intrusions as sites of mitochondrial contact

Padman BS, Lindblom R, Lazarou M

bioRxiv (2024)

DOI: 10.1083/jcb.202411138

Related EMDB entry:

Deposited:

2025-02-21

Released:

2025-11-25

Last modified:

2025-11-25

Imageset size:

32.75 GB

Imageset DOI:

10.6019/EMPIAR-12885

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
reconstructed volumes

Image Sets

1. Test ROI from Dataset 1 used for AIVE benchmarking.

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(740, 370)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.2552, 3.2552)

Details:

Test dataset (cropped from dataset 1) for AIVE benchmarking. Voxel values are inverted from original BSE signal. Spatial units are in nm. 10nm per slice.

Files:

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2. Raw model predictions & AIVE processed data for comparisons between 6 trained models

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(740, 370)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.2552, 3.2552)

Details:

All raw membrane predictions and AIVE processed data from Figures 1 & 2 of manuscript, showing direct comparison of results generated via different models. The trained models are RF (Random Forest), J48 (the java compatible extension of Ross Quinlan’s C4.5 classifier), MLP (Multi-Layer Perceptron), DT (Decision Table), JRip (java compatible propositional rule-based RIPPER), and PART (Projective Adaptive Resonance Theory neural network). 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)

3. Raw model predictions & human annotations for comparisons after AIVE processing

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(740, 370)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.2552, 3.2552)

Details:

Raw annotations and AIVE processed data for mitochondria from Figure 3, using classifications generated by one human on consecutive days, or two U-Nets with 3D anisotropic architecture (different random seeds).
Membrane predictions by a random forest model, which were used to conduct various forms of AIVE, are also provided.
Slice thickness is 10nm.

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

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4. Overview Dataset 1

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(2960, 720)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.5104, 6.5104)

Details:

Tiff stack for half-scale overview FIB-SEM dataset 1. 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. Overview Dataset 2

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(2930, 806)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.5104, 6.5104)

Details:

Tiff stack for half-scale overview FIB-SEM dataset 2. 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)

6. Overview Dataset 3

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(2948, 830)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(6.5104, 6.5104)

Details:

Tiff stack for half-scale overview FIB-SEM dataset 3. 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)

7. Overview Dataset 4 - Muscle

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(500, 500)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(16.0, 16.0)

Details:

Tiff stack for muscle tissue. Slice thickness is 20nm.

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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