EMPIAR-13391 - Cryo-ET dataset on lamellae of Dictyostelium discoideum cells acquired with various tilt-increments [multiple data sets in MRC format]

EMPIAR-13391

Cryo-ET dataset on lamellae of Dictyostelium discoideum cells acquired with various tilt-increments [multiple data sets in MRC format]

Publication:

Optimising the tilt-increment for in situ cryo-electron tomography

Tuijtel MW, Majtner M, Turoňová B, Beck M

eLife (---)

DOI: 10.7554/eLife.111639.1

Related EMDB entry:

Deposited:

2026-02-27

Released:

2026-07-27

Last modified:

2026-07-27

Imageset size:

707.53 GB

Imageset DOI:

10.6019/EMPIAR-13391

Experimental metadata:

Download xml json

Contains:

tilt series

Image Sets

1. Tilt-series on lamellae of Dictyostelium discoideum cells acquired with a 1-degree tilt increment

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.971, 1.971)

Details:

Tilt-series were aimed to collect 121 tilts, for some, fewer tilts were acquired. Tilt-series are sorted according to ascending tilt angle apart from -60 to +60 from lamella pre-tilt (8deg). mdoc files with metadata provided by SerialEM are also provided.
Tilt images that were discarded during processing are specified in "tilt_clean_1deg.txt".
Alignment results from IMOD are provided as TS_XXXX.xf files.
Tomograms that were used for STA are marked in tomo_list_1degree.txt.
Coordinates to raw ribosome particle picks by template matching are provided in TM_1degree_threshold5.star and TM_1degree_threshold6.star. Ribosome particle locations after M refinment are provided in M_1degree_particles.star.

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2. Tilt-series on lamellae of Dictyostelium discoideum cells acquired with a 2-degree tilt increment

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

119

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.971, 1.971)

Details:

Tilt-series were aimed to collect 61 tilts, for some, fewer tilts were acquired. Tilt-series are sorted according to ascending tilt angle apart from -60 to +60 from lamella pre-tilt (8deg). mdoc files with metadata provided by SerialEM are also provided.
Tilt images that were discarded during processing are specified in "tilt_clean_2deg.txt".
Alignment results from IMOD are provided as TS_XXXX.xf files.
Tomograms that were used for STA are marked in tomo_list_2degree.txt.
Coordinates to raw ribosome particle picks by template matching are provided in TM_2degree_threshold5.star and TM_2degree_threshold6.star. Ribosome particle locations after M refinment are provided in M_2degree_particles.star.

Files:

This entry cannot be downloaded from PDBj.

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. Tilt-series on lamellae of Dictyostelium discoideum cells acquired with a 3-degree tilt increment

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

120

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.971, 1.971)

Details:

Tilt-series were aimed to collect 41 tilts, for some, fewer tilts were acquired. Tilt-series are sorted according to ascending tilt angle apart from -60 to +60 from lamella pre-tilt (8deg). mdoc files with metadata provided by SerialEM are also provided.
Tilt images that were discarded during processing are specified in "tilt_clean_3deg.txt".
Alignment results from IMOD are provided as TS_XXXX.xf files.
Tomograms that were used for STA are marked in tomo_list_3degree.txt.
Coordinates to raw ribosome particle picks by template matching are provided in TM_3degree_threshold5.star and TM_3degree_threshold5.5.star. Ribosome particle locations after M refinment are provided in M_3degree_particles.star.

Files:

This entry cannot be downloaded from PDBj.

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. Tilt-series on lamellae of Dictyostelium discoideum cells acquired with a 5-degree tilt increment

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

122

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.971, 1.971)

Details:

Tilt-series were aimed to collect 25 tilts, for some, fewer tilts were acquired. Tilt-series are sorted according to ascending tilt angle apart from -60 to +60 from lamella pre-tilt (8deg). mdoc files with metadata provided by SerialEM are also provided.
Tilt images that were discarded during processing are specified in "tilt_clean_5deg.txt".
Alignment results from IMOD are provided as TS_XXXX.xf files.
Tomograms that were used for STA are marked in tomo_list_5degree.txt.
Coordinates to raw ribosome particle picks by template matching are provided in TM_5degree_threshold5.star. Ribosome particle locations after M refinment are provided in M_5degree_particles.star.

Files:

This entry cannot be downloaded from PDBj.

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. Tilt-series on lamellae of Dictyostelium discoideum cells acquired with a 10-degree tilt increment

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.971, 1.971)

Details:

Tilt-series were aimed to collect 13 tilts, for some, fewer tilts were acquired. Tilt-series are sorted according to ascending tilt angle apart from -60 to +60 from lamella pre-tilt (8deg). mdoc files with metadata provided by SerialEM are also provided.
Tilt images that were discarded during processing are specified in "tilt_clean_10deg.txt".
Alignment results from IMOD are provided as TS_XXXX.xf files.
Tomograms that were used for STA are marked in tomo_list_10degree.txt.
Coordinates to raw ribosome particle picks by template matching are provided in TM_10degree_threshold3.75.star. Ribosome particle locations after M refinment are provided in M_10degree_particles.star.

Files:

This entry cannot be downloaded from PDBj.

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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