{"EMPIAR-12905":{"imagesets":[{"segmentations":[],"name":"1 DIV rat cortical neuron tomograms high mag","directory":"data/1DIV_tomograms/1p24_apix_tomograms","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":11,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":1.24,"pixel_height":1.24,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"EMAN 2.99 used for reconstructions\n\nSpecific tomograms used in paper figures:\n-1day_ctrl_culture2_highMagImaged_04092025/Position_2,EMD-71859\n-1day_ctrl_culture2_highMagImaged_04092025/Position_13,EMD-71860\n-1day_ctrl_culture2_highMagImaged_04092025/Position_16,EMD-71861","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"1 DIV rat cortical neuron tomograms low mag","directory":"data/1DIV_tomograms/3p21_apix_tomograms","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":6,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":3.21,"pixel_height":3.21,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"EMAN 2.99 used for reconstructions\n\nSpecific tomograms/micrographs used in paper figures:\n-1day_ctrl_culture3_2_05222025/Position_34, EMD-71853\n-1day_ctrl_culture3_2_05222025/Position_35, EMD-71852\n-1day_ctrl_culture3_2_05222025/Position_25\n-1day_ctrl_culture3_2_05222025/Position_29","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"20 DIV rat cortical neuron tomograms high mag","directory":"data/20DIV_tomograms/1p24_apix_tomograms","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":17,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":1.24,"pixel_height":1.24,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"EMAN 2.99 used for reconstructions\n\nSpecific tomograms used in paper figures:\n-01252025_control/Position_2,EMD-71862\n-01252025_control/Position_8,EMD-71863\n-01252025_control/Position_14,EMD-71864","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"20 DIV rat cortical neuron tomograms low mag","directory":"data/20DIV_tomograms/3p21_apix_tomograms","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":14,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":3.21,"pixel_height":3.21,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"EMAN 2.99 used for reconstructions\nSpecific tomograms used in paper figures:\n-20day_ctrl_culture3_2_05252025/Position_4, EMD-71850\n-20day_ctrl_culture3_2_05252025/Position_5, EMD-71851","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"EGTA 5 min incubation rat cortical neuron micrographs","directory":"data/EGTA_exp_data/EGTA_data","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":185,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":3.21,"pixel_height":3.21,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Micrographs of 1DIV rat cortical neuron incubated for 1 hour in artificial cerebrospinal fluid and 10mM EGTA for 5 minutes prior to vitrification.\n\nwhen applicable:\n3def_5dose = -3 defocus, 5 electron dose images\n10def_10dose = -10 defocus, 10 electron dose images","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"aCSF control rat cortical neuron micrographs","directory":"data/EGTA_exp_data/aCSF_data","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":116,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":3.21,"pixel_height":3.21,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Micrographs of 1DIV rat cortical neuron incubated for 1 hour in artificial cerebrospinal fluid prior to vitrification. Serves as control to the neurons incubated in 10mM EGTA for 5 min.\n\nwhen applicable:\n3def_5dose = -3 defocus, 5 electron dose images\n10def_10dose = -10 defocus, 10 electron dose images","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"LDSAED octacalcium phosphate and 1 DIV rat cortical neuron aggregate micrographs","directory":"data/LDSAED","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":115,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":null,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Low dose selective area electron diffraction micrographs of 1DIV aggregate and 3hr Octacalcium phosphate elongated plate precipitates.\n\nNyquist spatial frequency = 1.75 Å-1\nCamera length = 670mm\nCollected on a 200kV glacios\n\nEMAN 2.99 used for analysis\nlsaed_analysis.ipynb = python notebook containing scripts used to process and analyze diffraction micrographs","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"Octacalcium phosphate tomograms","directory":"data/OCP_tomograms","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":20,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":3.21,"pixel_height":3.21,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Calcium phosphate precipitates collected after 3 hours of mixing. Generated as described previously in: Habraken, Wouter J E M et al. \"Ion-association complexes unite classical and non-classical theories for the biomimetic nucleation of calcium phosphate.\" Nature communications vol. 4 (2013): 1507. doi:10.1038/ncomms2490\n\nEMAN 2.99 used for reconstructions\n\nSpecific tomograms used in paper figures:\n-3hr_exp4_1_05182025/Position_11,EMD-71865\n-3hr_exp4_2_05222025/Position_1,EMD-71867\n-3hr_exp4_2_05222025/Position 4,EMD-71868","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"Waxham lab E18 rat hippocampal neuron aggregate","directory":"data/Waxham_ratHippocampal_ts","category":"tilt series","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":"UNSIGNED 16 BIT INTEGER","pixel_width":4.2,"pixel_height":4.2,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"","image_width":"3708","image_height":"3838"},{"segmentations":[],"name":"Aggregate area calculation experiment micrographs","directory":"data/area_calculation_exp","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":317,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":3.21,"pixel_height":3.21,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"These folders contain micrographs collected for calculating the area of the calcium phosphate aggregates from neurons under different conditions. \n\n3def_5dose = -3 defocus, 5 electron dose images\n10def_10dose = -10 defocus, 10 electron dose images\n\naggregate_area_calc.ipynb = python notebook containing scripts used to calculate the aggregate areas\nEMAN2 will need to be installed for it to run properly.\nEMAN 2.99 version used for this analysis","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"cryoCLEM micrographs","directory":"data/cryoCLEM","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":537,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":3.21,"pixel_height":3.21,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"3def_5dose = -3 defocus, 5 electron dose images\n10def_10dose = -10 defocus, 10 electron dose images\n\niFLM_raw_data folders contain the z stack fluorescent images generated with the Aquilos iFLM. \nglacios_image_sessions folders contain aggregate micrographs\nAssociated powerpoints in each subfolder contain fluorescent overview images.","image_width":"4096","image_height":"4096"}],"workflow_file":null,"grant_references":[{"funding_body":"National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)","code":"R35GM151999","country":"United States"},{"funding_body":"National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)","code":"F31NS132517","country":"United States"},{"funding_body":"National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)","code":"NS062829","country":"United States"},{"funding_body":"National Institutes of Health/National Institute of Mental Health (NIH/NIMH)","code":"MH137505","country":"United States"},{"funding_body":"National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)","code":"R01NS101686","country":"United States"},{"funding_body":"Beckman Foundation","code":"2021FIB-41","country":"United States"}],"version_history":[],"title":"Primary cortical neurons form calcium-phosphate sheets with a bone-precursor-like ultrastructure","principal_investigator":[{"author_orcid":"0000-0002-1903-1574","middle_name":"J.","organization":"Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine","street":null,"town_or_city":"Houston","state_or_province":null,"post_or_zip":"77030","telephone":null,"fax":null,"first_name":"Steven","last_name":"Ludtke","email":"sludtke [at] bcm.edu","country":"United States","entry":"EMPIAR-12905"},{"author_orcid":"0000-0001-5329-4629","middle_name":"David","organization":"Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine,","street":"1 Baylor Plaza","town_or_city":"Houston","state_or_province":"Texas","post_or_zip":"77030","telephone":null,"fax":null,"first_name":"Erik","last_name":"Anderson","email":"erikdavid [at] me.com","country":"United States","entry":"EMPIAR-12905"},{"author_orcid":"0000-0002-2092-920X","middle_name":null,"organization":"Department of Biochemistry and Molecular Pharmacology/Department of Neuroscience, Baylor College of Medicine,","street":"1 Baylor Plaza","town_or_city":"Houston","state_or_province":"Texas","post_or_zip":"77030","telephone":null,"fax":null,"first_name":"Kimberley","last_name":"Tolias","email":"tolias [at] bcm.edu","country":"United States","entry":"EMPIAR-12905"}],"status":"REL","deposition_date":"2025-07-28","release_date":"2026-07-22","obsolete_date":null,"update_date":"2026-07-22","corresponding_author":{"author":{"author_orcid":"0000-0002-1903-1574","middle_name":"J.","organization":"Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine","street":"1 Baylor Plaza","town_or_city":"Houston","state_or_province":"Texas","post_or_zip":"77030","first_name":"Steven","last_name":"Ludtke","country":"United States"}},"authors":[{"author":{"name":"Anderson ED","author_orcid":"0000-0001-5329-4629"}},{"author":{"name":"Ludtke SJ","author_orcid":"0000-0002-1903-1574"}}],"cross_references":["EMD-71863","EMD-71852","EMD-71853","EMD-71851","EMD-71850","EMD-71861","EMD-71859","EMD-71862","EMD-71864","EMD-71860"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Anderson ED","author_orcid":"0000-0001-5329-4629"},{"name":"Cronkite CA","author_orcid":"0000-0002-3276-9338"},{"name":"Baldwin PR","author_orcid":"0000-0002-4202-4129"},{"name":"Abella CP","author_orcid":"0009-0004-4362-4339"},{"name":"Duman JG","author_orcid":"0000-0002-6711-0656"},{"name":"Simmonds AN","author_orcid":"0009-0002-0169-0640"},{"name":"Waxham MN","author_orcid":"0000-0003-4801-1190"},{"name":"Tolias KF","author_orcid":"0000-0002-2092-920X"},{"name":"Ludtke SJ","author_orcid":"0000-0002-1903-1574"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Primary cortical neurons precipitate and extrude large mitochondria-associated calcium-phosphate sheets with a bone-precursor-like ultrastructure","volume":"19","country":"","first_page":null,"last_page":null,"year":"2026","language":"English","doi":"10.1186/s13041-025-01272-0","pubmedid":"41508094","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Molecular brain","journal_abbreviation":"Mol Brain","issue":"1","preprint":false}],"dataset_size":"1.5 TB","experiment_type":"EMDB","scale":"cell","entry_doi":"10.6019/EMPIAR-12905"}}