{"EMPIAR-11544":{"imagesets":[{"segmentations":[],"name":"Micrographs of untilted lamellae from cryo-FIB milled S. cerevisiae cells","directory":"data/images","category":"micrographs - single frame","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":30,"frames_per_image":50,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.06,"pixel_height":1.06,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Micrographs were recorded as movies on a Titan Krios at 300 keV equipped with a K3 direct detector and an energy filter, with an exposure rate of 1 e-/Å2 and a total exposure of 50 e-/Å2.","image_width":"5760","image_height":"4092"},{"segmentations":[],"name":"Scaled maximum intensity projections of SNR values obtained by 2D template matching with a large ribosomal subunit template","directory":"data/scaled_mips","category":"micrographs - single frame","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":30,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.06,"pixel_height":1.06,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Maximum intensity projections (MIPs) of the observed SNR values, scaled by subtracting the average SNR, and dividing by the standard deviation of the SNR per pixel. The MIPs display peaks in places where large ribosomal subunits were detected by 2D template matching. Peaks are associated with specific x,y locations, defocus and orientations of the targets that correspond with the matching template.","image_width":"5760","image_height":"4092"},{"segmentations":[],"name":"Template of S. cerevisiae large ribosomal subunit used for 2D template matching","directory":"data/template","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":1,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.06,"pixel_height":1.06,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"3D density maps used as templates in 2D template matching to detect large ribosomal subunits in the 2D images of lamellae of S. cerevisiae cells. The density maps were generated with the cryo-EM simulator implemented in cisTEM.","image_width":"384","image_height":"384"}],"workflow_file":null,"grant_references":[{"funding_body":"Chan Zuckerberg Initiative","code":"2021-234617 (5022)","country":"United States"}],"version_history":[],"title":"Quantification of gallium cryo-FIB milling damage in biological lamella","principal_investigator":[{"author_orcid":"0000-0001-9162-0421","middle_name":"Ayla","organization":"Department of Molecular and Cell Biology and Center for Computational Biology, University of California Berkeley","street":"University of California Berkeley","town_or_city":"Berkeley","state_or_province":"California","post_or_zip":"94720","telephone":"5852988506","fax":null,"first_name":"Bronwyn","last_name":"Lucas","email":"bronwynlucas [at] berkeley.edu","country":"United States","entry":"EMPIAR-11544"},{"author_orcid":"0000-0002-1506-909X","middle_name":null,"organization":"RNA Therapeutics Institute, and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School","street":"368 Plantation Street","town_or_city":"Worcester","state_or_province":"Massachusetts","post_or_zip":"01605","telephone":"+1 774-455-6682","fax":null,"first_name":"Nikolaus","last_name":"Grigorieff","email":"niko [at] grigorieff.org","country":"United States","entry":"EMPIAR-11544"}],"status":"REL","deposition_date":"2023-05-05","release_date":"2023-05-12","obsolete_date":null,"update_date":"2023-08-18","corresponding_author":{"author":{"author_orcid":"0000-0001-9162-0421","middle_name":"Ayla","organization":"Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology and Center for Computational Biology, University of Berkeley","street":"University of California Berkeley","town_or_city":"Berkeley","state_or_province":"California","post_or_zip":"94720","first_name":"Bronwyn","last_name":"Lucas","country":"United States"}},"authors":[{"author":{"name":"Lucas BA","author_orcid":"0000-0001-9162-0421"}},{"author":{"name":"Grigorieff N","author_orcid":"0000-0002-1506-909X"}}],"cross_references":[],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Lucas BA","author_orcid":"0000-0001-9162-0421"},{"name":"Grigorieff N","author_orcid":"0000-0002-1506-909X"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Quantification of gallium cryo-FIB milling damage in biological lamellae","volume":"120","country":"","first_page":null,"last_page":null,"year":"2023","language":"English","doi":"10.1073/pnas.2301852120","pubmedid":"37216561","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Proceedings of the National Academy of Sciences of the United States of America","journal_abbreviation":"Proc Natl Acad Sci U S A","issue":"23","preprint":false}],"dataset_size":"8.1 GB","experiment_type":"FIB-SEM","scale":"cell","entry_doi":"10.6019/EMPIAR-11544"}}