EMPIAR-13056 - Surface morphometrics reveals local membrane thickness variation in organellar subcompartments [multiple data sets in TIFF and MRC formats]

EMPIAR-13056

Surface morphometrics reveals local membrane thickness variation in organellar subcompartments [multiple data sets in TIFF and MRC formats]

Publication:

Surface morphometrics reveals local membrane thickness variation in organellar subcompartments

Medina M, Chang YT, Rahmani H, Fuentes D, Barad BA, Grotjahn DA

BioRxiv (2025)

PMID: 40654968

DOI: 10.1101/2025.04.30.651574

Related EMDB entry:

EMD-72321

Deposited:

2025-08-26

Released:

2025-11-19

Last modified:

2025-11-19

Imageset size:

575.36 GB

Imageset DOI:

10.6019/EMPIAR-13056

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
tilt series
reconstructed volumes

Image Sets

1. Raw unaligned frames and metadata for each tilt in tilt series acquired on lamellae from mouse embryonic fibroblasts

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

410

Image size:

(5760, 4092)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.663, 1.663)

Details:

Raw unaligned frames were preprocessed in Warp to generate tilt series stacks. Corresponding reference files in other directories under same base name (tilt series, mdocs, tomograms). Four directories included in subfolders. MIM019_2 and MIM019_3 are from mtGFP mouse embryonic fibroblasts (untreated). MIM029_3 and MIM032_1 are from mtGFP mouse embryonic fibroblasts treated with degraded Thapsigargin (500nm) for 8 hours- condition uncertain.

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2. Unaligned tilt series stacks from lamellae from mouse embryonic fibroblasts

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.663, 1.663)

Details:

The tilt series stacks (.st file) and rawtlt files (.rawtlt file) were created from Warp with the input of tilt-corrected mdoc files. Raw mdoc files are listed in the Tilt_series_mdoc folder. Tilt series stacks are then aligned in IMOD. MIM019_2 and MIM019_3 are from mtGFP mouse embryonic fibroblasts (untreated). MIM029_3 and MIM032_1 are from mtGFP mouse embryonic fibroblasts treated with degraded Thapsigargin (500nm) for 8 hours- condition uncertain.

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3. Reconstructed tomograms of lamellae from mouse embryonic fibroblasts

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1024, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(6.65, 6.65)

Details:

Bin4 tomograms are reconstructed from Warp after IMOD alignment. Particle coordinates for ATP synthase are provided in particle_list folder

Files:

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4. Reconstructed tomograms used for membrane thickness measurement of organelles in lamellae from mouse embryonic fibroblasts

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(682, 960)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(9.98, 9.98)

Details:

Bin 6 Warp reconstructed tomograms. Subset of MIM19_2, MIM019_3 used in thickness measurement analysis.

Files:

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5. Reconstructed tomograms used for segmentation of organelles in lamellae from mouse embryonic fibroblasts

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(512, 720)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.3, 13.3)

Details:

Bin 8 Warp reconstructed tomograms. Subset of MIM19_2, MIM019_3 used to generated organelle membrane segmentation. Associated segmentations files can be found in data/morphometrics_thickness/Voxel_segmentations. Associated triangulated surface meshes can be found in /data/morphometrics_thickness/Triangulated_surface_mesh.

Files:

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6. Raw unaligned frame and metadata for each tilt in tilt-series acquired on CHX-treated S. cerevisiae cryo-FIB lamellae

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

462

Image size:

(5760, 4092)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.663, 1.663)

Details:

Raw unaligned frames were preprocessed in Warp to generate tilt series stacks

Files:

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7. Unaligned tilt series stack of cryo-electron tomography acquired on CHX-treated S. cerevisiae cryo-FIB lamellae

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.663, 1.663)

Details:

The tilt series stacks (.st file) and rawtlt files (in Tilt_series_rawtlt) were created from Warp with the input of tilt-corrected mdoc files. Raw mdoc files are listed in the yeast/tilt_series_mdocs folder. Tilt series stacks are then aligned in IMOD.

Files:

This entry cannot be downloaded from PDBj.

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

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8. Reconstructed tomograms of CHX-treated S. cerevisiae lamellae used for segmentation of organelle membranes

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(682, 960)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(9.98, 9.98)

Details:

Bin 6 tomograms are reconstructed from Warp after IMOD alignment.

Files:

This entry cannot be downloaded from PDBj.

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9. Voxel segmentation of organelle membranes within in lamellae from mouse embryonic fibroblasts

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(512, 720)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.3, 13.3)

Details:

voxel segmentations from reconstructed tomograms at bin 8. These voxel segmentations were then input into surface morphometrics to generate triangulated surface meshes.

Files:

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PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modeling and machine learning.

Costa-Gomes B, Greer J, Juraschko N, Parkhurst J, Mirecka J, Famili M, Rangel-Smith C, Strickson O, Lowe A, Basham M, Burnley T. (2025)

CryoEMNet driven symmetry-aware molecular reconstruction through deep learning enhanced electron microscopy.

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Self-supervised learning for generalizable particle picking in cryo-EM micrographs.

Zamanos A, Koromilas P, Bouritsas G, Kastritis PL, Panagakis Y. (2025)

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