{"EMPIAR-11063":{"imagesets":[{"segmentations":[],"name":"Unaligned multi-frame micrographs of ER-HoxB8 lamella","directory":"data","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":4647,"frames_per_image":33,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":0.6667,"pixel_height":0.6667,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"For each lamella a cisTEM project is provided. Raw movies are under /data/???_Lamella?/Assets/Movies/*.tif. The SerialEM metadata and gain references are in the same folder.","image_width":"11520","image_height":"8184"},{"segmentations":[],"name":"Aligned micrographs of ER-HoxB8 lamella","directory":"data","category":"micrographs - single frame","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":4647,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.5,"pixel_height":1.5,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"For each lamella a cisTEM project is provided. Aligned micrographs are under /data/???_Lamella?/Assets/Images/*_0.mrc. Since each micrographs is cropped to the beam, the dimensions are different for every micrograph. A mask that indicated the illuminated area is provided for each micropgraph under *_mask.mrc","image_width":null,"image_height":null},{"segmentations":[],"name":"2DTM results of micrographs of ER-HoxB8 lamella","directory":"data","category":"stitched maps","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":4647,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.5,"pixel_height":1.5,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"2DTM results can be found in the /data/???_Lamella?/Assets/TemplateMatching/ folder. For each image there are several mrc files that encode SNR, defocus, psi, theta, and phi at each pixel. To reduce file size pixels where the scaled SNR was below 6.5 (substantially below detection threshold) were set to 0 and the files were compressed using zstd.","image_width":null,"image_height":null},{"segmentations":[],"name":"Stitched maps of lamellae imaged using DeCo-LACE - Overview","directory":"data/deco_lace_processing/refined_assembly_it2","category":"stitched maps","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":8,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":75.0,"pixel_height":75.0,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Stitched maps of lamellae made from individual DeCo-LACE exposures. The files ???_Lamella?_montage_t2_tophat.tif were resampled to 75A pixel size and the exposure was flattened using a top-hat filter.","image_width":null,"image_height":null},{"segmentations":[],"name":"Stitched maps of lamellae imaged using DeCo-LACE - High resolution","directory":"data/deco_lace_processing/refined_assembly_it2","category":"stitched maps","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":8,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":7.5,"pixel_height":7.5,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Stitched maps of lamellae made from individual DeCo-LACE exposures. The files ???_Lamella?_montage_t2_highres.tif were resampled to 7.5A pixel size.","image_width":"14010","image_height":"17082"}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"Cryo-EM data and 2DTM results of entire sections of differentiated ER-HoxB8 cells","principal_investigator":[{"author_orcid":"0000-0002-9911-706X","middle_name":null,"organization":"RTI, UMass Chan Medical School, Worcester, MA","street":"55 Lake Avenue North","town_or_city":"Worcester","state_or_province":"Massachusetts","post_or_zip":"01655","telephone":null,"fax":null,"first_name":"Johannes","last_name":"Elferich","email":"johannes.elferich [at] umassmed.edu","country":"United States","entry":"EMPIAR-11063"}],"status":"REL","deposition_date":"2022-06-01","release_date":"2023-02-01","obsolete_date":null,"update_date":"2023-02-13","corresponding_author":{"author":{"author_orcid":"0000-0002-9911-706X","middle_name":null,"organization":"RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA","street":"55 Lake Avenue North","town_or_city":"Worcester","state_or_province":"Massachusetts","post_or_zip":"01655","first_name":"Johannes","last_name":"Elferich","country":"United States"}},"authors":[{"author":{"name":"Elferich JE","author_orcid":"0000-0002-9911-706X"}},{"author":{"name":"Schiroli GS","author_orcid":"0000-0002-9812-8728"}},{"author":{"name":"Scadden DS","author_orcid":null}},{"author":{"name":"Grigorieff NG","author_orcid":"0000-0002-1506-909X"}}],"cross_references":[],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Elferich J","author_orcid":"0000-0002-9911-706X"},{"name":"Schiroli G","author_orcid":"0000-0001-9821-7133"},{"name":"Scadden DT","author_orcid":"0000-0002-9812-8728"},{"name":"Grigorieff N","author_orcid":"0000-0002-1506-909X"}],"editors":[{"name":" ","author_orcid":null}],"published":true,"j_or_nj_citation":true,"title":"Defocus Corrected Large Area Cryo-EM (DeCo-LACE) for label-free detection of molecules across entire cell sections","volume":"11","country":"","first_page":null,"last_page":null,"year":"2022","language":"English","doi":"10.7554/elife.80980","pubmedid":"36382886","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"eLife","journal_abbreviation":"Elife","issue":null,"preprint":false},{"authors":[{"name":"Elferich JE","author_orcid":"0000-0002-9911-706X"},{"name":"Schiroli GS","author_orcid":"0000-0002-9812-8728"},{"name":"Scadden DS","author_orcid":null},{"name":"Grigorieff NG","author_orcid":"0000-0002-1506-909X"}],"editors":[{"name":" ","author_orcid":null}],"published":true,"j_or_nj_citation":true,"title":"Defocus Corrected Large Area Cryo-EM (DeCo-LACE) for Label-Free Detection of Molecules across Entire Cell Sections","volume":null,"country":"","first_page":null,"last_page":null,"year":null,"language":null,"doi":"10.1101/2022.06.13.495969","pubmedid":null,"details":"For each lamella a cisTEM project is provided, containing Gatan K3 movies, motion-corrected images, and 2DTM results.","book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"bioRxiv","journal_abbreviation":"","issue":null,"preprint":true}],"dataset_size":"1.3 TB","experiment_type":"Exception","scale":"cell","entry_doi":"10.6019/EMPIAR-11063"}}