{"EMPIAR-10464":{"imagesets":[{"segmentations":[],"name":"Survey SBF SEM images showing the position of the imaged ROIs at the start of each run (3 runs- #20-22)","directory":"data/Survey_images","category":"micrographs - single frame","header_format":"DM4","data_format":"DM4","num_images_or_tilt_series":3,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":null,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Survey images showing the position of the ROIs imaged for each run, if opened in Digital Micrograph. \nVariable pixel widths and heights. Run 20: 5000 x 5000, run 21-22: 4096 x 4096. Variable pixel widths. Run 20: 75.6nm, run 21: 87.2nm, run 22: 86.3nm","image_width":null,"image_height":null},{"segmentations":[],"name":"Low magnification raw SBF SEM overview images (ROI00) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain over 3 runs (20-22)","directory":"data/P400_SBF_SEM_F1S1_run20-22_EMPIAR-10464/ROI00","category":"micrographs - single frame","header_format":"DM4","data_format":"DM4","num_images_or_tilt_series":1099,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":null,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Low magnification overview SBF SEM images (ROI00) for runs 20-22, linked to higher magnification images in ROI01 and ROI02. Imaged at 2kV, 2us dwell, variable pressure 5Pa. \nVariable pixel widths and heights. Run 20: 7500 x 5497, run 21: 7000 x 4000, run 22: 6000 x 4000. Variable pixel widths. Run 20: 48.5nm, run 21: 54nm, run 22: 49nm.","image_width":null,"image_height":null},{"segmentations":[],"name":"High magnification raw SBF SEM images (ROI01) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain over 3 runs (20-22)","directory":"data/P400_SBF_SEM_F1S1_run20-22_EMPIAR-10464/ROI01","category":"micrographs - single frame","header_format":"DM4","data_format":"DM4","num_images_or_tilt_series":1099,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":null,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"High magnification images (ROI01) linked to lower magnification images in ROI00, for 3 runs (20-22). Imaged at 2kV, 2us dwell, variable pressure 5Pa.\nVariable pixel widths and heights. Run 20: 16384 x 16384, run 21: 15000 x 10000, run 22: 15000 x 12000. Variable pixel widths. Run 20: 6.6nm, run 21-22: 5.8nm.","image_width":null,"image_height":null},{"segmentations":[],"name":"High magnification raw SBF SEM images (ROI02) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain (run 20)","directory":"data/P400_SBF_SEM_F1S1_run20-22_EMPIAR-10464/run20_ROI02","category":"micrographs - single frame","header_format":"DM4","data_format":"DM4","num_images_or_tilt_series":391,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":69.0,"pixel_height":69.0,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"High magnification images (ROI02) linked to lower magnification images in ROI00 for run 20. Imaged at 2kV, 2us dwell, variable pressure 5Pa.","image_width":"8192","image_height":"8192"},{"segmentations":[],"name":"High magnification raw SBF SEM images (ROI02) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain for runs 21-22","directory":"data/P400_SBF_SEM_F1S1_run20-22_EMPIAR-10464/run21-22_ROI02","category":"micrographs - single frame","header_format":"DM4","data_format":"DM4","num_images_or_tilt_series":705,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":null,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"High magnification images (ROI02) linked to lower magnification images in ROI00 for run 21-22. Note that it is a different ROI than ROI02-run 20. Imaged at 2kV, 2us dwell, variable pressure 5Pa. \nVariable pixel widths and heights. Run 21: 4000 x 4000, run 22: 5000 x 5000. Variable pixel widths. Run 21: 7.1nm, run 22: 6.2nm.","image_width":null,"image_height":null}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"SBF SEM images of a Zebrafish hindbrain containing several Toxoplasma gondii tachizoites at different stages of replication","principal_investigator":[{"author_orcid":"0000-0002-5703-2922","middle_name":null,"organization":"Francis Crick Institute, Electron Microscopy STP","street":"1 Midland Road","town_or_city":"London","state_or_province":"London","post_or_zip":"NW1 1AT","telephone":null,"fax":null,"first_name":"Marie-Charlotte","last_name":"Domart","email":"marie-charlotte.domart [at] crick.ac.uk","country":"United Kingdom","entry":"EMPIAR-10464"}],"status":"REL","deposition_date":"2020-07-03","release_date":"2021-10-27","obsolete_date":null,"update_date":"2022-02-08","corresponding_author":{"author":{"author_orcid":"0000-0002-5703-2922","middle_name":null,"organization":"Francis Crick Institute, Electron Microscopy STP","street":"1 Midland Road","town_or_city":"London","state_or_province":"London","post_or_zip":"NW1 1AT","first_name":"Marie-Charlotte","last_name":"Domart","country":"United Kingdom"}},"authors":[{"author":{"name":"Peddie CJ","author_orcid":null}},{"author":{"name":"Domart MC","author_orcid":"0000-0002-5703-2922"}},{"author":{"name":"Collinson L","author_orcid":null}}],"cross_references":[],"biostudies_references":[{"name":"S-BSST429"}],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Yoshida N","author_orcid":"0000-0002-3925-8557"},{"name":"Domart MC","author_orcid":"0000-0002-5703-2922"},{"name":"Peddie CJ","author_orcid":null},{"name":"Yakimovich A","author_orcid":"0000-0003-2458-4904"},{"name":"Mazon-Moya MJ","author_orcid":null},{"name":"Hawkins TA","author_orcid":"0000-0003-2921-0004"},{"name":"Collinson L","author_orcid":null},{"name":"Mercer J","author_orcid":null},{"name":"Frickel EM","author_orcid":"0000-0002-9515-3442"},{"name":"Mostowy S","author_orcid":"0000-0002-7286-6503"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"The zebrafish as a novel model for the <i>in vivo</i> study of <i>Toxoplasma gondii</i> replication and interaction with macrophages","volume":"13","country":"","first_page":null,"last_page":null,"year":"2020","language":"English","doi":"10.1242/dmm.043091","pubmedid":"32461265","details":"Raw data corresponding to Suppl. Fig 2, Suppl. Fig 4 and Suppl. Fig. 6 in the paper","book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Disease models & mechanisms","journal_abbreviation":"Dis Model Mech","issue":"7","preprint":false}],"dataset_size":"553.9 GB","experiment_type":"CLEM","scale":null,"entry_doi":"10.6019/EMPIAR-10464"}}