EMPIAR-11561 - Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells [multiple data sets in TIFF and MRC formats]

EMPIAR-11561

Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells [multiple data sets in TIFF and MRC formats]

Publication:

Genetically encoded multimeric tags for subcellular protein localisation in cryo-EM

Fung HKH, Hayashi Y, Salo VT, Babenko A, Zagoriy I, Brunner A, Ellenberg J, Müller CW, Cuylen-Haering S, Mahamid J

(---)

Related EMDB entry:

EMD-18194 EMD-16303

Deposited:

2022-12-07

Released:

2023-09-05

Last modified:

2023-09-05

Imageset size:

174.19 GB

Imageset DOI:

10.6019/EMPIAR-11561

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
tilt series
reconstructed volumes

Image Sets

1. Unaligned multi-frame micrographs for dataset 1 (211206)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

118

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.425, 3.425)

Details:

Unaligned multi-frame micrographs (frames/*.tif) corresponding to 2 tilt series with corresponding gain reference, defect map and metadata (mdoc/*.mdoc). Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

ダウンロードするファイル数やサイズによっては、膨大な時間がかかります。また、この機能は不安定で正常に動作しない可能性があり、ダウンロードされたファイルのチェックサムは検証されません。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

2. Tilt series and alignment information for dataset 1 (211206)

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.425, 3.425)

Details:

Tilt series following motion correction in WARP (*.st), with tilt angle information (*.rawtlt) for tilt series alignment in AreTomo and alignment solutions outputted by AreTomo (*.aln and *.xf). Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

3. Reconstructed tomograms for dataset 1 (211206)

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1022, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.7, 13.7)

Details:

Tomograms (*.mrc) reconstructed by weighted back-projection in AreTomo and 4-times binned, and coordinates from subtomogram averaging of GEM2 particles (*.star). Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

4. Unaligned multi-frame micrographs for dataset 2 (220330)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

178

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.425, 3.425)

Details:

Unaligned multi-frame micrographs (frames/*.tif) corresponding to 3 tilt series with corresponding gain reference, defect map and metadata (mdoc/*.mdoc). Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. See README.md under 'All Files' for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

5. Tilt series and alignment information for dataset 2 (220330)

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.425, 3.425)

Details:

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

6. Reconstructed tomograms for dataset 2 (220330)

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1022, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.7, 13.7)

Details:

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

7. Unaligned multi-frame micrographs for dataset 3 (220504)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(3710, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(3.3701, 3.3701)

Details:

Unaligned multi-frame micrographs (frames/*.tif) corresponding to 1 tilt series with corresponding gain reference, defect map and metadata (mdoc/*.mdoc). Data acquired with Volta phase plate on a K2 Summit detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

8. Tilt series and alignment information for dataset 3 (220504)

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(3710, 3838)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.3701, 3.3701)

Details:

Tilt series following motion correction in WARP (*.st), with tilt angle information (*.rawtlt) for tilt series alignment in AreTomo and alignment solutions outputted by AreTomo (*.aln and *.xf). Data acquired with Volta phase plate on a K2 Summit detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

9. Reconstructed tomograms for dataset 3 (220504)

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(958, 926)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.4804, 13.4804)

Details:

Tomograms (*.mrc) reconstructed by weighted back-projection in AreTomo and 4-times binned, and coordinates from subtomogram averaging of GEM2 particles (*.star). Data acquired with Volta phase plate on a K2 Summit detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

10. Unaligned multi-frame micrographs for dataset 4 (220506)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

293

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.425, 3.425)

Details:

Unaligned multi-frame micrographs (frames/*.tif) corresponding to 5 tilt series with corresponding gain reference, defect map and metadata (mdoc/*.mdoc). Data acquired with Volta phase plate on a K3 BioQuantum detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

11. Tilt series and alignment information for dataset 4 (220506)

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.425, 3.425)

Details:

Tilt series following motion correction in WARP (*.st), with tilt angle information (*.rawtlt) for tilt series alignment in AreTomo and alignment solutions outputted by AreTomo (*.aln and *.xf). Data acquired with Volta phase plate on a K3 BioQuantum detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

12. Reconstructed tomograms for dataset 4 (220506)

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1022, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.7, 13.7)

Details:

Tomograms (*.mrc) reconstructed by weighted back-projection in AreTomo and 4-times binned, and coordinates from subtomogram averaging of GEM2 particles (*.star). Data acquired with Volta phase plate on a K3 BioQuantum detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

13. Unaligned multi-frame micrographs for dataset 5 (220720)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

340

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.425, 3.425)

Details:

Unaligned multi-frame micrographs (frames/*.tif) corresponding to 6 tilt series with corresponding gain reference, defect map and metadata (mdoc/*.mdoc). Data acquired with Volta phase plate on a K3 BioQuantum detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

14. Tilt series and alignment information for dataset 5 (220720)

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.425, 3.425)

Details:

Tilt series following motion correction in WARP (*.st), with tilt angle information (*.rawtlt) for tilt series alignment in AreTomo and alignment solutions outputted by AreTomo (*.aln and *.xf). Data acquired with Volta phase plate on a K3 BioQuantum detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

15. Reconstructed tomograms for dataset 5 (220720)

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1022, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.7, 13.7)

Details:

Tomograms (*.mrc) reconstructed by weighted back-projection in AreTomo and 4-times binned, and coordinates from subtomogram averaging of GEM2 particles (*.star). Data acquired with Volta phase plate on a K3 BioQuantum detector. See README.md under All Files for more information (also copied below).

# Cryo-electron tomography of GEM2-labelled Mito-EGFP in HeLa cells

Five independent cryo-ET datasets were collected. Each dataset is organised under the following directory structure, with the directories "data/", "alignment/", and "tomograms/" each designated as an Image Set.

- data/
- CountRef.mrc gain reference
- defects.tif defect map (K3 data only)
- frames/ unaligned, unbinned multi-frame micrographs
- mdoc/ MDOC files listing exposure dose, pixel size and tilt angle information for each tilt
- alignment/
- TS_###.mrc/
- TS_###.mrc.st sorted, motion-corrected tilt series from WARP
- TS_###.mrc.rawtlt tilt angle information corresponding to tilt series
- TS_###.mrc.aln AreTomo tilt series alignment solution
- TS_###.mrc.xf XF file from AreTomo alignment
- mdoc_edited/ MDOC files with entries for discarded tilts during alignment removed
- tomograms/
- *.mrc tomograms reconstructed by weighted back-projection in AreTomo, 4-times binned
- ######.star combined STAR file listing the refined coordinates of GEM2 particles at 6.85 A/px in this dataset

Acquisition parameters differ for each dataset and are specified below. Tilt series were aligned in AreTomo 1.3.1 with the following parameters: 8 by 6 patches (K3 data) or 6 by 6 patches (K2 data), VolZ 2000, AlignZ 1000, TiltAxis ## -1 (as calibrated for the magnification and microsco
pe used), TiltCor 0.

## Dataset 1 (211206) - Image Sets 1 to 3

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 2 tilt series. Pixel size, 3.425 A/px.

## Dataset 2 (220330) - Image Sets 4 to 6

Data acquired with defocus only, no Volta phase plate, on a K3 BioQuantum detector. 3 tilt series. Pixel size, 3.425 A/px.

## Dataset 3 (220504) - Image Sets 7 to 9

Data acquired with Volta phase plate on a K2 Summit detector. 1 tilt series. Pixel size, 3.3701 A/px.

## Dataset 4 (220506) - Image Sets 10 to 12

Data acquired with Volta phase plate on a K3 BioQuantum detector. 5 tilt series. Pixel size, 3.425 A/px.

## Dataset 5 (220720) - Image Sets 13 to 15

Data acquired with Volta phase plate on a K3 BioQuantum detector. 6 tilt series. Pixel size, 3.425 A/px.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

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Citations

A variational framework with composite sparse regularization for cryo-electron tomography reconstruction.

Yu C, Xu Z, Zeng Q, Wan X, El-Messiry H, Zhang F, Han R. (2026)

CryoFSL: an annotation-efficient, few-shot learning framework for robust protein particle picking in cryo-electron microscopy micrographs.

Poudel B, Gyawali R, Dhakal A, Cheng J, Xu D. (2026)

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking.

Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.

He L, Bartesaghi A. (2026)

Unbend, correction of local beam-induced sample motion in cryo-EM images using a 3D spline model.

Kong L, Zottig X, Elferich J, Grigorieff N. (2026)

Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

Fonseca N, Duraisamy AK, Wang Z, Somasundharam S, Tayebinia M, de Oliveira LC, Ma M, Turner J, Patwardhan A, Kleywegt GJ, Hartley M, Morris KL. (2026)

CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

Dual site targeting of the bacterial 70S ribosome by tetracyclines.

Devarkar SC, Lomakin IB, Wang J, Grada A, Bunick CG. (2026)

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.

Jones HN, Deshmukh A, Pande K. (2026)

CryoGS: High-Quality Cryo-EM Homogeneous Reconstruction by Gaussian Splatting

Zeng B, Liu S, Cheng S, Xu G, Fan H. (2026)

See all citations

Protein Data Bank Japan News

[2026-06-10]

333件のPDBエントリーが新たに公開されました。（2026-06-10付）