{"EMPIAR-10989":{"imagesets":[{"segmentations":[],"name":"Raw unaligned multi-frame micrographs for each tilt in tilt-series acquired on RPE1 cryo-FIB lamellae","directory":"data/frames","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":179,"frames_per_image":8,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":3.3702,"pixel_height":3.3702,"micrographs_file_pattern":"data/frames/0004_001_0.0.tif","picked_particles_file_pattern":"","picked_particles_directory":"","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.","image_width":"3838","image_height":"3710"},{"segmentations":[{"file":"data/labels/00004_actin_ground_truth.mrc","description":"Comprehensive ground truth segmentation volume (32 bit floats, 928x960, 13.48 A voxel size) of actin for tomogram 00004.","original_files":"data/tomograms/00004_sq_df_sorted.rec","original_format":"","entry":null},{"file":"data/labels/00004_MT_ground_truth.mrc","description":"Comprehensive ground truth segmentation volume (32 bit floats, 928x960, 13.48 A voxel size) of microtubules (MT) for tomogram 00004.","original_files":"data/tomograms/00004_sq_df_sorted.rec","original_format":"","entry":null},{"file":"data/labels/00011_actin_ground_truth.mrc","description":"Comprehensive ground truth segmentation volume (32 bit floats, 928x960, 13.48 A voxel size) of actin for tomogram 00011.","original_files":"data/tomograms/00011_sq_df_sorted.rec","original_format":"","entry":null},{"file":"data/labels/00012_actin_ground_truth.mrc","description":"Comprehensive ground truth segmentation volume (32 bit floats, 928x960, 13.48 A voxel size) of actin for tomogram 00012.","original_files":"data/tomograms/00012_sq_df_sorted.rec","original_format":"","entry":null}],"name":"Reconstructed cryo-electron tomograms acquired on RPE1 cryo-FIB lamellae","directory":"data/tomograms","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":3,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"SIGNED BYTE","pixel_width":13.48,"pixel_height":13.48,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","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). \nComprehensive 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. \nActin ground truth coordinates (xml files, in Å) produced in Amira provided in corresponding actin_ground_truth_coordinates folder.\nFiltered 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).","image_width":"928","image_height":"928"},{"segmentations":[],"name":"Tilt series stacks and metadata of cryo-electron tomograms acquired on RPE1 cryo-FIB lamellae","directory":"data/metadata","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":3,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"SIGNED 16 BIT INTEGER","pixel_width":3.3702,"pixel_height":3.3702,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","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).","image_width":"3708","image_height":"3708"}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"Cryo-electron tomograms of RPE1 cells with comprehensive annotation of actin filaments and microtubules","principal_investigator":[{"author_orcid":"0000-0001-6968-041X","middle_name":null,"organization":"European Molecular Biology Laboratory","street":null,"town_or_city":"Heidelberg","state_or_province":null,"post_or_zip":"69117","telephone":null,"fax":null,"first_name":"Julia","last_name":"Mahamid","email":"julia.mahamid [at] embl.de","country":"Germany","entry":"EMPIAR-10989"}],"status":"REL","deposition_date":"2022-02-23","release_date":"2022-11-23","obsolete_date":null,"update_date":"2022-11-23","corresponding_author":{"author":{"author_orcid":"0000-0001-6968-041X","middle_name":null,"organization":"European Molecular Biology Laboratory","street":null,"town_or_city":"Heidelberg","state_or_province":null,"post_or_zip":"69117","first_name":"Julia","last_name":"Mahamid","country":"Germany"}},"authors":[{"author":{"name":"Cheng DWC","author_orcid":null}},{"author":{"name":"Goetz SK","author_orcid":"0000-0002-9903-3667"}},{"author":{"name":"Mahamid J","author_orcid":"0000-0001-6968-041X"}}],"cross_references":["EMD-16136"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Teresa I","author_orcid":"0000-0002-4691-9501"},{"name":"Goetz SK","author_orcid":"0000-0002-9903-3667"},{"name":"Cheng DWC","author_orcid":"0000-0003-1545-0269"},{"name":"Zaugg JB","author_orcid":"0000-0001-8324-4040"},{"name":"Mahamid J","author_orcid":"0000-0001-6968-041X"}],"editors":[],"published":false,"j_or_nj_citation":true,"title":"Convolutional networks for supervised mining of molecular patterns within cellular context","volume":null,"country":"","first_page":null,"last_page":null,"year":null,"language":null,"doi":null,"pubmedid":null,"details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"","journal_abbreviation":"","issue":null,"preprint":false},{"authors":[{"name":"Vignaud T","author_orcid":"0000-0001-7434-914X"},{"name":"Copos C","author_orcid":null},{"name":"Leterrier C","author_orcid":"0000-0002-2957-2032"},{"name":"Toro-Nahuelpan M","author_orcid":"0000-0001-5333-3640"},{"name":"Tseng Q","author_orcid":null},{"name":"Mahamid J","author_orcid":"0000-0001-6968-041X"},{"name":"Blanchoin L","author_orcid":"0000-0001-8146-9254"},{"name":"Mogilner A","author_orcid":"0000-0002-9310-3812"},{"name":"Théry M","author_orcid":"0000-0002-9968-1779"},{"name":"Kurzawa L","author_orcid":"0000-0002-2990-3305"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Stress fibres are embedded in a contractile cortical network","volume":"20","country":"","first_page":"410","last_page":"420","year":"2020","language":"English","doi":"10.1038/s41563-020-00825-z","pubmedid":"33077951","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Nature materials","journal_abbreviation":"Nat Mater","issue":"3","preprint":false},{"authors":[{"name":"Toro-Nahuelpan M","author_orcid":"0000-0001-5333-3640"},{"name":"Zagoriy I","author_orcid":null},{"name":"Senger F","author_orcid":null},{"name":"Blanchoin L","author_orcid":"0000-0001-8146-9254"},{"name":"Théry M","author_orcid":"0000-0002-9968-1779"},{"name":"Mahamid J","author_orcid":"0000-0001-6968-041X"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies","volume":"17","country":"","first_page":"50","last_page":"54","year":"2019","language":"English","doi":"10.1038/s41592-019-0630-5","pubmedid":"31740821","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Nature methods","journal_abbreviation":"Nat Methods","issue":"1","preprint":false}],"dataset_size":"32.9 GB","experiment_type":"EMDB","scale":"molecule","entry_doi":"10.6019/EMPIAR-10989"}}