EMPIAR-10989
Cryo-electron tomograms of RPE1 cells with comprehensive annotation of actin filaments and microtubules [multiple data sets in TIFF and MRC formats]
Publication:

Convolutional networks for supervised mining of molecular patterns within cellular context

Teresa I, Goetz SK, Cheng DWC, Zaugg JB, Mahamid J

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Related EMDB entry:
Deposited:
2022-02-23
Released:
2022-11-23
Last modified:
2022-11-23
Imageset size:
32.92 GB
Imageset DOI:
Experimental metadata:
Contains:
  • micrographs - multiframe
  • reconstructed volumes
  • tilt series
1. Raw unaligned multi-frame micrographs for each tilt in tilt-series acquired on RPE1 cryo-FIB lamellae
Category:
micrographs - multiframe
Image format:
TIFF
No. of images or tilt series:
179
Image size:
(3838, 3710)
Pixel type:
UNSIGNED 16 BIT INTEGER
Pixel spacing:
(3.3702, 3.3702)
Details:
Raw, unaligned multi-frame micrographs were aligned into tilt series stacks (st files in metadata folder) and tomograms reconstructed using etomo (IMOD) (rec files in tomgrams folder). Naming for TS_011 and TS_012 corresponds to prefix 00011 and 00012 in all other folders. Corresponding count reference files (dm4 file) are located in the frames folder. Frames per image varies from 8 to 12.
Files:
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2. Reconstructed cryo-electron tomograms acquired on RPE1 cryo-FIB lamellae
Category:
reconstructed volumes
Image format:
MRC
No. of images or tilt series:
3
Image size:
(928, 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).
Comprehensive ground truth segmentation volumes (32 bit floats, 928x960, 13.48 Å voxel size) of actin for all 3 tomograms and of microtubules (MT) for tomogram 0004 are provided in labels folder.
Actin ground truth coordinates (xml files, in Å) produced in Amira provided in corresponding actin_ground_truth_coordinates folder.
Filtered tomograms (amplitude spectrum matching filter, DeePiCt) provided in tomograms/filtered_tomos folder used for actin predictions (post-processed in labels/predictions folder, raw output in labels/predictions_probability_map folder).
Files:
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3. Tilt series stacks and metadata of cryo-electron tomograms acquired on RPE1 cryo-FIB lamellae
Category:
tilt series
Image format:
MRC
No. of images or tilt series:
3
Image size:
(3708, 3708)
Pixel type:
SIGNED 16 BIT INTEGER
Pixel spacing:
(3.3702, 3.3702)
Details:
Tilt series stacks (st files) from aligned frame stacks (in frames folder), tilt series alignment files (xf from etomo, IMOD) and acquisition metadata files (mdoc files) to reconstruct tomograms (in tomograms folder).
Files:
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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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