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- EMDB-71629: Comparison of fully-sampled and sparse cryo-STEM tomography 3D re... -

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Basic information

Entry
Database: EMDB / ID: EMD-71629
TitleComparison of fully-sampled and sparse cryo-STEM tomography 3D reconstructions
Map data3D SIRT reconstruction of DCT inpainted sparse (66%) cryo-STEM tilt-series on E. coli cell 1
Sample
  • Cell: Whole E. coli cryo-tomography
KeywordsE. coli / bacteria / UNKNOWN FUNCTION
Biological speciesEscherichia coli (E. coli)
Methodelectron tomography / cryo EM
AuthorsTrepout S
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE42-0001 France
CitationJournal: Ultramicroscopy / Year: 2026
Title: About the alignment and 3D reconstruction of sparse cryo-scanning transmission electron tomography datasets.
Authors: Sylvain Trépout /
Abstract: In electron microscopy, sparse imaging consists in the collection of a limited subset of the image pixels, which can be used to reduce electron beam damage. Scanning transmission electron microscopy ...In electron microscopy, sparse imaging consists in the collection of a limited subset of the image pixels, which can be used to reduce electron beam damage. Scanning transmission electron microscopy (STEM) is particularly adapted to sparse imaging owing to the scanning nature of the method, scan patterns can be designed where fewer sample locations are targeted. However, since some of the pixels are not scanned, there is an inherent loss of information. Several algorithms were developed to reconstruct missing pixels with high fidelity. Whereas sparse imaging and missing pixel reconstruction in 2D experiments are mature methods, the application of sparse imaging in 3D scanning transmission electron tomography (STET) is rare and still under development. The main difficulty encountered in tomography studies is the tilt-series alignment, which must be accurate to ensure high-quality 3D reconstruction. Because sparse images contain only a certain portion of the original information, the images constituting sparse tilt-series might not share enough mutual information to guarantee an accurate alignment, even after missing pixel reconstruction. This work presents for the first time a thorough analysis of the fiducial alignment and reconstruction of sparse (cryo-)STET tilt-series. Furthermore, the limits of sparse imaging are explored to estimate the minimum amount of information required to obtain good-quality 3D reconstructions. The use of a cryo-fixed biological sample is motivated by the fact that cryo-samples are typical highly beam-sensitive samples, and that the intricate nature and structure complexity of biological samples place them among the most difficult ones to reconstruct with high details.
History
DepositionJul 7, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71629.png

Downloads & links

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Map

FileDownload / File: emd_71629.map.gz / Format: CCP4 / Size: 683.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D SIRT reconstruction of DCT inpainted sparse (66%) cryo-STEM tilt-series on E. coli cell 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
40 Å/pix.
x 400 pix.
= 16000. Å		40 Å/pix.
x 700 pix.
= 28000. Å		40 Å/pix.
x 640 pix.
= 25600. Å

Projections

Slices (1/3)

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Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 40 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-4.617276 - 1.3960353
Average (Standard dev.)0.13880327 (±0.2459189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-50
Dimensions700640400
Spacing640700400
CellA: 25600.0 Å / B: 28000.0 Å / C: 16000.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_1.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 4
Projections & Slices
AxesZYX

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Histogram

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Additional map: 3D SIRT reconstruction of DCT inpainted sparse (75%)...

Fileemd_71629_additional_10.map
Annotation3D SIRT reconstruction of DCT inpainted sparse (75%) cryo-STEM tilt-series on E. coli cell 2
Projections & Slices
AxesZYX

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Density Histograms

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_11.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 2
Projections & Slices
AxesZYX

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Histogram

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_2.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of DCT inpainted sparse (66%)...

Fileemd_71629_additional_3.map
Annotation3D SIRT reconstruction of DCT inpainted sparse (66%) cryo-STEM tilt-series on E. coli cell 4
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of DCT inpainted sparse (75%)...

Fileemd_71629_additional_4.map
Annotation3D SIRT reconstruction of DCT inpainted sparse (75%) cryo-STEM tilt-series on E. coli cell 5
Projections & Slices
AxesZYX

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Histogram

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_5.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 5
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of DCT inpainted sparse (80%)...

Fileemd_71629_additional_6.map
Annotation3D SIRT reconstruction of DCT inpainted sparse (80%) cryo-STEM tilt-series on E. coli cell 6
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_7.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of DCT inpainted sparse (80%)...

Fileemd_71629_additional_8.map
Annotation3D SIRT reconstruction of DCT inpainted sparse (80%) cryo-STEM tilt-series on E. coli cell 3
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_9.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 3
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Sample components

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Entire : Whole E. coli cryo-tomography

EntireName: Whole E. coli cryo-tomography
Components
  • Cell: Whole E. coli cryo-tomography

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Supramolecule #1: Whole E. coli cryo-tomography

SupramoleculeName: Whole E. coli cryo-tomography / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Details: M9 media
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 20 nm

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Electron microscopy

MicroscopeJEOL 2200FS
DetailsAlignment on the Ronchigram
Image recordingFilm or detector model: OTHER / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.2 µm
Sample stageSpecimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

DetailsJEOL BF STEM Detector
Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: TOMO3D / Number images used: 40
CTF correctionDetails: This is STEM / Type: NONE

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