EMPIAR-10988
Defocus and Volta potential phase plate cryo-electron tomography of S. pombe cryo-FIB lamellae with comprehensive annotations of structures and macromolecules [multiple data sets in TIFF and MRC formats]
Publication:

Convolutional networks for supervised mining of molecular patterns within cellular context

Teresa I, Goetz SK, Mahamid J, Zaugg JB

(---)

Deposited:
2021-09-21
Released:
2022-11-17
Last modified:
2022-11-17
Imageset size:
305.46 GB
Imageset DOI:
Experimental metadata:
Contains:
  • micrographs - multiframe
  • reconstructed volumes
  • tilt series
1. Raw unaligned multi-frame micrographs for each tilt in 10 tilt-series acquired with defocus-only (DEF) on S. pombe cryo-FIB lamellae
Category:
micrographs - multiframe
Image format:
TIFF
No. of images or tilt series:
510
Image size:
(3838, 3710)
Pixel type:
UNSIGNED 16 BIT INTEGER
Pixel spacing:
(3.3702, 3.3702)
Details:
Raw unaligned multi-frame micrographs were aligned, sorted and combined into tilt series stacks using Warp (st files in metadata folder) and tomograms reconstructed using etomo (IMOD) (rec files in tomgrams folder). Naming from TS_026 to TS_045 corresponds to TS_0011 to TS_0020 in the original publication.
Original metadata files (mdocs_ori) and the count ref file (dm4 file) are provided in the frames folder.
Files:
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2. Reconstructed cryo-electron tomograms acquired with defocus-only (DEF) on S. pombe cryo-FIB lamellae
Category:
reconstructed volumes
Image format:
MRC
No. of images or tilt series:
10
Image size:
(960, 928)
Pixel type:
SIGNED 16 BIT INTEGER
Pixel spacing:
(13.48, 13.48)
Details:
Tomograms (4-times binned reconstructions, original pixel size 3.3702 Å) from aligned frame stacks (st files in metadata folder, tif files in frames folder), mdoc and xf alignment files (in metadata folder). Naming from TS_026 to TS_045 corresponds to TS_0011 to TS_0020 in the original publication.
For each of the 10 tomograms, comprehensive segmentation volumes (32 bit floats, 928x960, 13.48 Å voxel size) of ribosomes, fatty acid synthase (FAS), membranes, organelles (labels) and cytosol are provided in the labels folder. Voxel labels of individual organelles in labels files are defined in organelle_labels.txt.
Ribosome and FAS particle coordinates (csv files) are provided in the corresponding particle_lists folder (in csv files with x, y, z coordinates in columns 1, 2, 3 respectively, 4-times binned pixels with original pixel size 3.3702 Å).
Files:
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3. Tilt series stacks and metadata of cryo-electron tomograms acquired with defocus-only (DEF) on S. pombe cryo-FIB lamellae
Category:
tilt series
Image format:
MRC
No. of images or tilt series:
10
Image size:
(3708, 3838)
Pixel type:
32 BIT FLOAT
Pixel spacing:
(3.3702, 3.3702)
Details:
Tilt series stacks (st files from Warp) from aligned frame stacks (in frames folder), tilt series alignment files (xf from etomo, IMOD) and acquisition metadata files modified to match tilt series stacks (in mdocs_modified) to reconstruct tomograms (in tomograms folder). Naming from TS_026 to TS_045 corresponds to TS_0011 to TS_0020 in the original publication.
Files:
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4. Raw unaligned multi-frame micrographs for each tilt in10 tilt-series acquired with a Volta potential phase plate (VPP) and defocus on S. pombe cryo-FIB lamellae
Category:
micrographs - multiframe
Image format:
TIFF
No. of images or tilt series:
510
Image size:
(3838, 3710)
Pixel type:
UNSIGNED 16 BIT INTEGER
Pixel spacing:
(3.3702, 3.3702)
Details:
Raw unaligned multi-frame micrographs were aligned, sorted and combined into tilt series stacks using Warp (st files in metadata folder) and tomograms reconstructed using etomo (IMOD) (rec files in tomgrams folder).
Original metadata files (mdocs_ori) and two count reference files, one for tilt series 1 to 4 and 10, and one for tilt series 5 to 9 (dm4 files) are provided in the frames folder.
Files:
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5. Reconstructed cryo-electron tomograms acquired with a Volta potential phase plate (VPP) and defocus on S. pombe cryo-FIB lamellae
Category:
reconstructed volumes
Image format:
MRC
No. of images or tilt series:
10
Image size:
(960, 928)
Pixel type:
SIGNED BYTE
Pixel spacing:
(13.48, 13.48)
Details:
Tomograms (4-times binned reconstructions, original pixel size 3.3702 Å) from aligned frame stacks (st files in metadata folder, tif files in frames folder), mdoc and xf alignment files (in metadata folder).
For each of the 10 tomograms, comprehensive segmentation volumes (32 bit floats, 928x960, 13.48 Å voxel size) of ribosomes, fatty acid synthase (FAS), membranes, organelles (labels) and cytosol are provided in the labels folder. Voxel labels of individual organelles in labels files are defined in organelle_labels.txt.
Ribosome and FAS particle coordinates (csv files) are provided in the corresponding particle_lists folder (in csv files with x, y, z coordinates in in columns 1, 2, 3 respectively, 4-times binned pixels with original pixel size 3.3702 Å).
Files:
Loading...
6. Tilt series stacks and metadata of cryo-electron tomograms acquired with a Volta potential phase plate (VPP) and defocus on S. pombe cryo-FIB lamellae
Category:
tilt series
Image format:
MRC
No. of images or tilt series:
10
Image size:
(3708, 3838)
Pixel type:
32 BIT FLOAT
Pixel spacing:
(3.3702, 3.3702)
Details:
Tilt series stacks (st files from Warp) from aligned frame stacks (in frames folder), tilt series alignment files (xf from etomo, IMOD) and acquisition metadata files modified to match tilt series stacks (in mdocs_modified) to reconstruct tomograms (in tomograms folder).
Files:
Loading...
Files:
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Citations
Liu T, Shilliday F, Cook AD, Zeeshan M, Brady D, Tewari R, Sutherland CJ, Roberts AJ, Moores CA. (2022)
Jespersen N, Ehrenbolger K, Winiger RR, Svedberg D, Vossbrinck CR, Barandun J. (2022)
Sheng Y, Harrison PJ, Vogirala V, Yang Z, Strain-Damerell C, Frosio T, Himes BA, Siebert CA, Zhang P, Clare DK. (2022)
See all citations
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