EMPIAR-10982 - Seven benchmark datasets of instance segmentation of mitochondria: 6 diverse volume EM + 1 TEM (100 images) datasets [multiple data sets in TIFF format]

EMPIAR-10982

Seven benchmark datasets of instance segmentation of mitochondria: 6 diverse volume EM + 1 TEM (100 images) datasets [multiple data sets in TIFF format]

Publication:

Six benchmark volumes of instance segmentation of mitochondria from diverse volume EM datasets

Narayan K, Conrad RW

(---)

Related EMDB entry:

Deposited:

2022-03-11

Released:

2022-03-15

Last modified:

2022-10-04

Imageset size:

4.12 GB

Imageset DOI:

10.6019/EMPIAR-10982

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame

Image Sets

1. C. elegans benchmark volume of instance segmentation of mitochondria: grayscale image file + label map file

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(256, 256)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(240.0, 240.0)

Details:

---

Files:

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

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

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)

2. Fly brain benchmark volume of instance segmentation of mitochondria: grayscale image file + label map file

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(255, 255)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(120.0, 120.0)

Details:

---

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. Glycolytic muscle benchmark volume of instance segmentation of mitochondria: grayscale image file + label map file

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

Image size:

(765, 383)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(180.0, 180.0)

Details:

---

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. HeLa cell benchmark volume of instance segmentation of mitochondria: grayscale image file + label map file

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(256, 256)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(150.0, 150.0)

Details:

---

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. Lucchi++ neuronal benchmark volume of instance segmentation of mitochondria: grayscale image file + label map file

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(1024, 768)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

---

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. Salivary gland (rat) benchmark volume of instance segmentation of mitochondria: grayscale image file + label map file

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(1200, 1081)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(150.0, 150.0)

Details:

---

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. TEM 100 image benchmark dataset of instance segmentation of mitochondria: grayscale image file + label map file

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

100

Image size:

(1024, 1024)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

100 TEM images of cellular features (most but not all images are 1024 x 1024, pixel size in low nm range) and corresponding 2D instance segmentation label maps of mitochondria from a variety of imaging projects. A .csv file of available metadata is also included

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)

Browse All Files

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)

Quick Links

Talks and Tutorials

EMPIAR Quick tour

Statistics

Publications

Re-use case study

EMPIAR in the news

Claim entries to your ORCiD

COVID-19 Data Portal

EMDB

PDBe

BioImage Archive

EMNavigator@PDBj

PDBj

RCSB@PDBj

EMDataResoruce@RCSB,EMDB,NCMI

Citations

Structural basis for HIV-1 antagonism of host APOBEC3G via Cullin E3 ligase.

Ito F, Alvarez-Cabrera AL, Liu S, Yang H, Shiriaeva A, Zhou ZH, Chen XS. (2023)

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection.

Rigden DJ, Fernández XM. (2023)

EMPIAR: the Electron Microscopy Public Image Archive.

Iudin A, Korir PK, Somasundharam S, Weyand S, Cattavitello C, Fonseca N, Salih O, Kleywegt GJ, Patwardhan A. (2023)

CLEMSite, a software for automated phenotypic screens using light microscopy and FIB-SEM.

Serra Lleti JM, Steyer AM, Schieber NL, Neumann B, Tischer C, Hilsenstein V, Holtstrom M, Unrau D, Kirmse R, Lucocq JM, Pepperkok R, Schwab Y. (2023)

Structure of a RecT/Redβ family recombinase in complex with a duplex intermediate of DNA annealing.

Caldwell BJ, Norris AS, Karbowski CF, Wiegand AM, Wysocki VH, Bell CE. (2022)

See all citations

Protein Data Bank Japan News

[2024-04-24]

354 new PDB entries have been released on 2024-04-24.

[2024-04-09]

[wwPDB] CASP16 Call for Targets

[2024-04-02]

Announcement of the PDBj Newsletter Vol.24 release

[2024-03-21]

[wwPDB] Paper Published on NMR Restraint Validation

[2024-03-13]

[wwPDB] Paper Published on CryoEM Archiving and Validation Recommendations

[2024-03-06]

[wwPDB] Poster Prize Awarded at The Biophysical Society Meeting

[2024-02-15]

Notice of Service Suspension (ASH, DASH, SeSAW, MAFFTash, Spanner, SFAS)

[2024-02-13]

[wwPDB] Biocurator Milestone: >10,000 Depositions Processed

[2024-02-06]

[wwPDB] Preprint Published on NMR Restraint Validation

[2024-02-05]

[wwPDB] Preprint Published on CryoEM Archiving and Validation Recommendations

See all news