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.

Files:

このエントリはPDBjからダウンロードすることはできません。

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 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:

このエントリはPDBjからダウンロードすることはできません。

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. 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:

このエントリはPDBjからダウンロードすることはできません。

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. 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:

このエントリはPDBjからダウンロードすることはできません。

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 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:

このエントリはPDBjからダウンロードすることはできません。

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)

Browse All Files

Quick Links

Browse EMPIAR

Sample Preparation Widget

Volume Browser

Tomo Viewer Prototype

Claim entries to your ORCiD

Talks and Tutorials

EMPIAR Quick tour

Publications

Re-use study

Statistics

EMPIAR in the news

COVID-19 Data Portal

EMDB

BioImage Archive

PDBe

EMNavigator@PDBj

PDBj

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)

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

He L, Bartesaghi A. (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)

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

[2026-07-23]

[wwPDB] PDBの大きな変更まであと1年：拡張PDB ID、PDBベータアーカイブ、PDBx/mmCIF