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

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

(---)

Related EMDB entry:

EMD-16136

Deposited:

2022-02-23

Released:

2022-11-23

Last modified:

2022-11-23

Imageset size:

32.92 GB

Imageset DOI:

10.6019/EMPIAR-10989

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
reconstructed volumes
tilt series

Image Sets

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:

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:

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:

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

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

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