REL
2022-02-23
2022-11-23
2022-11-23
Cryo-electron tomograms of RPE1 cells with comprehensive annotation of actin filaments and microtubules
0000-0001-6968-041X
Julia
Mahamid
European Molecular Biology Laboratory
Heidelberg
Germany
69117
0000-0001-6968-041X
Julia
Mahamid
European Molecular Biology Laboratory
Heidelberg
Germany
69117
Cheng DWC
Goetz SK
Mahamid J
32.9
10.6019/EMPIAR-10989
EMDB
molecule
EMD-16136
Teresa I
Goetz SK
Cheng DWC
Zaugg JB
Mahamid J
Convolutional networks for supervised mining of molecular patterns within cellular context
Vignaud T
Copos C
Leterrier C
Toro-Nahuelpan M
Tseng Q
Mahamid J
Blanchoin L
Mogilner A
Théry M
Kurzawa L
Stress fibres are embedded in a contractile cortical network
Nature materials
Nat Mater
3
20
410
420
2020
English
10.1038/s41563-020-00825-z
33077951
Toro-Nahuelpan M
Zagoriy I
Senger F
Blanchoin L
Théry M
Mahamid J
Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies
Nature methods
Nat Methods
1
17
50
54
2019
English
10.1038/s41592-019-0630-5
31740821
Raw unaligned multi-frame micrographs for each tilt in tilt-series acquired on RPE1 cryo-FIB lamellae
/data/frames
micrographs - multiframe
TIFF
TIFF
179
8
UNSIGNED 16 BIT INTEGER
3838
3.3702
3710
3.3702
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.
data/frames/0004_001_0.0.tif
Reconstructed cryo-electron tomograms acquired on RPE1 cryo-FIB lamellae
/data/tomograms
reconstructed volumes
MRC
MRC
3
1
SIGNED BYTE
928
13.48
928
13.48
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).
data/labels/00004_actin_ground_truth.mrc
Comprehensive ground truth segmentation volume (32 bit floats, 928x960, 13.48 A voxel size) of actin for tomogram 00004.
data/tomograms/00004_sq_df_sorted.rec
data/labels/00004_MT_ground_truth.mrc
Comprehensive ground truth segmentation volume (32 bit floats, 928x960, 13.48 A voxel size) of microtubules (MT) for tomogram 00004.
data/tomograms/00004_sq_df_sorted.rec
data/labels/00011_actin_ground_truth.mrc
Comprehensive ground truth segmentation volume (32 bit floats, 928x960, 13.48 A voxel size) of actin for tomogram 00011.
data/tomograms/00011_sq_df_sorted.rec
data/labels/00012_actin_ground_truth.mrc
Comprehensive ground truth segmentation volume (32 bit floats, 928x960, 13.48 A voxel size) of actin for tomogram 00012.
data/tomograms/00012_sq_df_sorted.rec
Tilt series stacks and metadata of cryo-electron tomograms acquired on RPE1 cryo-FIB lamellae
/data/metadata
tilt series
MRC
MRC
3
1
SIGNED 16 BIT INTEGER
3708
3.3702
3708
3.3702
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).