{"EMPIAR-11695":{"imagesets":[{"segmentations":[],"name":"Unprocessed FIB-SEM slices acquired from Cal51 wt cells (Sample A)","directory":"data/SampleA_Cal51_wt/1_RawUnprocessedFrames","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":598,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":3.372396,"pixel_height":3.372396,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.","image_width":"6144","image_height":"4096"},{"segmentations":[],"name":"Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 wt cells (Sample A)","directory":"data/SampleA_Cal51_wt/2_PreprocessedAIVEinputs","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":5,"frames_per_image":598,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Inputs used to calculate AIVE results for Cal51 wt cells (Sample A), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the \"MATTER\" & \"MEMB\" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.","image_width":"3002","image_height":"909"},{"segmentations":[],"name":"AIVE outputs generated from FIB-SEM data of Cal51 wt cells (Sample A).","directory":"data/SampleA_Cal51_wt/3_AIVEoutputs","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":51,"frames_per_image":598,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"AIVE outputs generated for FIB-SEM data acquired from Cal51 wt cells (Sample A), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, \"Mitos\"; Peroxisomes, \"Perox\"; Endosomes, \"EndoCyt & EndoLys\"; Endoplasmic reticulum, \"ER\"; Golgi Apparatus, \"Golgi\"; Vesicles, \"Vesicles\"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided (\"IndividualFilledMitochondria\"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.","image_width":"3002","image_height":"909"},{"segmentations":[],"name":"Unprocessed FIB-SEM slices acquired from Cal51 PEX26ko cells (Sample B)","directory":"data/SampleB_Cal51_PEX26ko/1_RawUnprocessedFrames","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":520,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":3.372396,"pixel_height":3.372396,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.","image_width":"6144","image_height":"4096"},{"segmentations":[],"name":"Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 PEX26ko cells (Sample B)","directory":"data/SampleB_Cal51_PEX26ko/2_PreprocessedAIVEinputs","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":5,"frames_per_image":520,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Inputs used to calculate AIVE results for Cal51 PEX26ko cells (Sample B), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the \"MATTER\" & \"MEMB\" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.","image_width":"2884","image_height":"1075"},{"segmentations":[],"name":"AIVE outputs generated from FIB-SEM data of Cal51 PEX26ko cells (Sample B)","directory":"data/SampleB_Cal51_PEX26ko/3_AIVEoutputs","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":85,"frames_per_image":520,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"AIVE outputs generated for FIB-SEM data acquired from Cal51 PEX26ko cells (Sample B), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, \"Mitos\"; Peroxisomes, \"Perox\"; Endosomes, \"EndoCyt & EndoLys\"; Endoplasmic reticulum, \"ER\"; Golgi Apparatus, \"Golgi\"; Vesicles, \"Vesicles\"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided (\"IndividualFilledMitochondria\"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.","image_width":"2884","image_height":"1075"},{"segmentations":[],"name":"Unprocessed FIB-SEM slices acquired from Cal51 GOLGA5ko cells (Sample C)","directory":"data/SampleC_Cal51_GOLGA5KO/1_RawUnprocessedFrames","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":520,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":3.372396,"pixel_height":3.372396,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.","image_width":"6144","image_height":"4096"},{"segmentations":[],"name":"Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 GOLGA5ko cells (Sample C)","directory":"data/SampleC_Cal51_GOLGA5KO/2_PreprocessedAIVEinputs","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":5,"frames_per_image":527,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Inputs used to calculate AIVE results for Cal51 GOLGA5ko cells (Sample C), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the \"MATTER\" & \"MEMB\" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.","image_width":"2579","image_height":"1026"},{"segmentations":[],"name":"AIVE outputs generated from FIB-SEM data of Cal51 GOLGA5ko cells (Sample C)","directory":"data/SampleC_Cal51_GOLGA5KO/3_AIVEoutputs","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":79,"frames_per_image":527,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"AIVE outputs generated for FIB-SEM data acquired from Cal51 GOLGA5ko cells (Sample C), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, \"Mitos\"; Peroxisomes, \"Perox\"; Endosomes, \"EndoCyt & EndoLys\"; Endoplasmic reticulum, \"ER\"; Golgi Apparatus, \"Golgi\"; Vesicles, \"Vesicles\"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided (\"IndividualFilledMitochondria\"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.","image_width":"2579","image_height":"1026"},{"segmentations":[],"name":"Unprocessed FIB-SEM slices acquired from Cal51 GOLGA8Mko cells (Sample D)","directory":"data/SampleD_Cal51_GOLGA8MKO/1_RawUnprocessedFrames","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":502,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":3.372396,"pixel_height":3.372396,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.","image_width":"6144","image_height":"4096"},{"segmentations":[],"name":"Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 GOLGA8Mko cells (Sample D)","directory":"data/SampleD_Cal51_GOLGA8MKO/2_PreprocessedAIVEinputs","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":5,"frames_per_image":502,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Inputs used to calculate AIVE results for Cal51 GOLGA8Mko cells (Sample D), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the \"MATTER\" & \"MEMB\" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.","image_width":"2922","image_height":"1158"},{"segmentations":[],"name":"AIVE outputs generated from FIB-SEM data of Cal51 GOLGA8Mko cells (Sample D)","directory":"data/SampleD_Cal51_GOLGA8MKO/3_AIVEoutputs","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":49,"frames_per_image":502,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"AIVE outputs generated for FIB-SEM data acquired from Cal51 GOLGA8Mko cells (Sample D), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, \"Mitos\"; Peroxisomes, \"Perox\"; Endosomes, \"EndoCyt & EndoLys\"; Endoplasmic reticulum, \"ER\"; Golgi Apparatus, \"Golgi\"; Vesicles, \"Vesicles\"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided (\"IndividualFilledMitochondria\"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.","image_width":"2922","image_height":"1158"},{"segmentations":[],"name":"Unprocessed FIB-SEM slices acquired from Cal51 SEC61A2ko cells (Sample E)","directory":"data/SampleE_Cal51_SEC61A2KO/1_RawUnprocessedFrames","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":528,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":3.372396,"pixel_height":3.372396,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.","image_width":"6144","image_height":"4096"},{"segmentations":[],"name":"Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 SEC61A2ko cells (Sample E)","directory":"data/SampleE_Cal51_SEC61A2KO/2_PreprocessedAIVEinputs","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":5,"frames_per_image":528,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Inputs used to calculate AIVE results for Cal51 SEC61A2ko cells (Sample E), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the \"MATTER\" & \"MEMB\" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.","image_width":"3003","image_height":"1356"},{"segmentations":[],"name":"AIVE outputs generated from FIB-SEM data of Cal51 SEC61A2ko cells (Sample E)","directory":"data/SampleE_Cal51_SEC61A2KO/3_AIVEoutputs","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":60,"frames_per_image":528,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"AIVE outputs generated for FIB-SEM data acquired from Cal51 SEC61A2ko cells (Sample E), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, \"Mitos\"; Peroxisomes, \"Perox\"; Endosomes, \"EndoCyt & EndoLys\"; Endoplasmic reticulum, \"ER\"; Golgi Apparatus, \"Golgi\"; Vesicles, \"Vesicles\"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided (\"IndividualFilledMitochondria\"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.","image_width":"3003","image_height":"1356"},{"segmentations":[],"name":"Unprocessed FIB-SEM slices acquired from Cal51 SEC62ko cells (Sample F)","directory":"data/SampleF_Cal51_SEC62KO/1_RawUnprocessedFrames","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":654,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":3.372396,"pixel_height":3.372396,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw FIB-SEM backscatter electron micrographs acquired using a Helios NanoLab G3 CX. Slice thickness is 10nm.","image_width":"6144","image_height":"4096"},{"segmentations":[],"name":"Preprocessed inputs for AIVE (AI-directed Voxel Extraction) of Cal51 SEC62ko cells (Sample F)","directory":"data/SampleF_Cal51_SEC62KO/2_PreprocessedAIVEinputs","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":5,"frames_per_image":654,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Inputs used to calculate AIVE results for Cal51 SEC62ko cells (Sample F), including: The FIB-SEM data after image registration, cropping, rescale, and value inversion for assessment during organelle classification (RegisteredScaledInvertedCropped), the normalized denoized signal inputs (CLAHE_PREPROC), label image identifying organelles (ClassIDLabels), AI predictions for the \"MATTER\" & \"MEMB\" (Membrane) classes (MATTER_MLpredictions & MEMBS_MLpredictions). All images have a 10nm slice interval.","image_width":"2910","image_height":"1236"},{"segmentations":[],"name":"AIVE outputs generated from FIB-SEM data of Cal51 SEC62ko cells (Sample F)","directory":"data/SampleF_Cal51_SEC62KO/3_AIVEoutputs","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":56,"frames_per_image":654,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":6.744792,"pixel_height":6.744792,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"AIVE outputs generated for FIB-SEM data acquired from Cal51 SEC62ko cells (Sample F), including the raw AIVE outputs generated for each class of organelle used for analysis (Mitochondria, \"Mitos\"; Peroxisomes, \"Perox\"; Endosomes, \"EndoCyt & EndoLys\"; Endoplasmic reticulum, \"ER\"; Golgi Apparatus, \"Golgi\"; Vesicles, \"Vesicles\"), which have been provided as a compressed archive. Filled individual mitochondria used for bulk morphometric analyses are also provided (\"IndividualFilledMitochondria\"), as is the blender (.BLEND) file used to generate 3D renders of the dataset overview.","image_width":"2910","image_height":"1236"}],"workflow_file":null,"grant_references":[{"funding_body":"National Health and Medical Research Council (NHMRC, Australia)","code":"APP 2010332","country":"Australia"}],"version_history":[],"title":"Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network","principal_investigator":[{"author_orcid":"0000-0002-6998-8403","middle_name":null,"organization":"University of Western Australia","street":"6 Verdun Street","town_or_city":"Perth","state_or_province":"Western Australia","post_or_zip":"6009","telephone":null,"fax":null,"first_name":"Aleksandra","last_name":"Filipovska","email":"aleksandra.filipovska [at] uwa.edu.au","country":"Australia","entry":"EMPIAR-11695"}],"status":"REL","deposition_date":"2023-09-18","release_date":"2023-10-09","obsolete_date":null,"update_date":"2023-10-09","corresponding_author":{"author":{"author_orcid":"0000-0002-6998-8403","middle_name":null,"organization":"University of Western Australia","street":"6 Verdun Street","town_or_city":"Perth","state_or_province":"Western Australia","post_or_zip":"6009","first_name":"Aleksandra","last_name":"Filipovska","country":"Australia"}},"authors":[{"author":{"name":"Lee RG","author_orcid":"0000-0002-3292-7914"}},{"author":{"name":"Rudler DL","author_orcid":"0000-0002-5540-6548"}},{"author":{"name":"Raven SA","author_orcid":null}},{"author":{"name":"Peng L","author_orcid":null}},{"author":{"name":"Chopin A","author_orcid":"0009-0006-0390-6723"}},{"author":{"name":"Moh ESX","author_orcid":"0000-0003-4289-0147"}},{"author":{"name":"McCubbin T","author_orcid":"0000-0002-9707-6532"}},{"author":{"name":"Siira SJ","author_orcid":"0000-0002-8391-0143"}},{"author":{"name":"Fagan SV","author_orcid":"0009-0002-3817-587X"}},{"author":{"name":"DeBono NJ","author_orcid":"0000-0001-5452-3008"}},{"author":{"name":"Stentenbach M","author_orcid":"0000-0002-1933-9149"}},{"author":{"name":"Browne J","author_orcid":"0000-0002-1413-2026"}},{"author":{"name":"Rackham FF","author_orcid":null}},{"author":{"name":"Li J","author_orcid":null}},{"author":{"name":"Simpson KJ","author_orcid":"0000-0001-9136-1781"}},{"author":{"name":"Marcellin E","author_orcid":"0000-0003-3173-7956"}},{"author":{"name":"Packer NH","author_orcid":"0000-0002-7532-4021"}},{"author":{"name":"Reid GE","author_orcid":"0000-0002-9675-1444"}},{"author":{"name":"Padman BS","author_orcid":"0000-0002-5710-6100"}},{"author":{"name":"Rackham O","author_orcid":"0000-0002-5301-9624"}},{"author":{"name":"Filipovska A","author_orcid":"0000-0002-6998-8403"}}],"cross_references":[],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Lee RG","author_orcid":"0000-0002-3292-7914"},{"name":"Rudler DL","author_orcid":"0000-0002-5540-6548"},{"name":"Raven SA","author_orcid":null},{"name":"Peng L","author_orcid":null},{"name":"Chopin A","author_orcid":"0009-0006-0390-6723"},{"name":"Moh ESX","author_orcid":"0000-0003-4289-0147"},{"name":"McCubbin T","author_orcid":"0000-0002-9707-6532"},{"name":"Siira SJ","author_orcid":"0000-0002-8391-0143"},{"name":"Fagan SV","author_orcid":"0009-0002-3817-587X"},{"name":"DeBono NJ","author_orcid":"0000-0001-5452-3008"},{"name":"Stentenbach M","author_orcid":"0000-0002-1933-9149"},{"name":"Browne J","author_orcid":"0000-0002-1413-2026"},{"name":"Rackham FF","author_orcid":null},{"name":"Li J","author_orcid":null},{"name":"Simpson KJ","author_orcid":"0000-0001-9136-1781"},{"name":"Marcellin E","author_orcid":"0000-0003-3173-7956"},{"name":"Packer NH","author_orcid":"0000-0002-7532-4021"},{"name":"Reid GE","author_orcid":"0000-0002-9675-1444"},{"name":"Padman BS","author_orcid":"0000-0002-5710-6100"},{"name":"Rackham O","author_orcid":"0000-0002-5301-9624"},{"name":"Filipovska A","author_orcid":"0000-0002-6998-8403"}],"editors":[],"published":false,"j_or_nj_citation":true,"title":"Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network","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":"Nature cell Biology","journal_abbreviation":"Nat. cell Biol.","issue":null,"preprint":false}],"dataset_size":"434.2 GB","experiment_type":"FIB-SEM","scale":"cell","entry_doi":"10.6019/EMPIAR-11695"}}