Cryo-electron tomograms of RPE1 cells with comprehensive annotation of actin filaments and microtubules

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).