{"EMPIAR-12850":{"imagesets":[{"segmentations":[{"file":"data/EM2B6","description":"The filenames adhere to a structured naming convention that includes:\n\nExperiment ID (266): An experiment-specific ID.\nAcquisition Date (e.g., 221116, 240326): Indicates when the image was captured or processed (YYMMDD format).\nMicroscope (JEM1400): Specifies the use of a Jeol JEM-1400 Flash TEM.\nSample Type (Slot###): Denotes the specific grid and section number, e.g., \"Slot812\" for Grid Box Position 8, Grid 1, Section 2.\nPixel/Voxel Size (xy###nm): Represents the resolution of the image in nanometers.\nAdditional Modifiers (e.g., _img, _seg, _labels, _z##, _x##_y##): These provide further details about the file content:\n_img: Raw image data.\n_seg: Segmented data, often showing specific structures like nuclei.\n_labels: Labeled image data, usually associated with segmentation.\n_z##, _x##, _y##: Indicate specific slice numbers or coordinates within a 3D volume, particularly for tomograms.\n.tif or .zarr: File format, where .tif is a common image format and .zarr is a cloud-native, chunked array format suitable for large datasets.","original_files":null,"original_format":null,"entry":null}],"name":"Transmission electron micrograph and segmentation","directory":"data/EM2B6","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","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":null,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"TEM Imaging and Data Acquisition\n\nSection TEM Mapping\nEntire sections were imaged using a Jeol JEM-1400 Flash TEM at an acceleration voltage of 80 kV. Limitless Panorama montaging software was used to acquire typical montages of 400×400 µm2 with a pixel size of 340 nm (X/Y).\n\nRegion of Interest (ROI) TEM Mapping\nHigh-resolution images of regions around the ROI were acquired using the same TEM parameters as for section mapping, except the typical montage size was 70×100 µm2 with a pixel size of 3.4 nm (X/Y).\n\nTEM Tomography\nFor 3D reconstruction, regions around the ROI were imaged using a Jeol JEM-1400 Flash TEM at an acceleration voltage of 120 kV. Tilt series were acquired using SerialEM.9 The typical reconstructed volume was 4×4×0.2 µm3 with a voxel size of 1.8 nm. Tomograms were reconstructed using IMOD software.\n\nFile Naming Convention\nFiles are named according to the following structure:\n{ExperimentID}_{AcquisitionDate}_{Microscope}_{SampleType}_{PixelSize}.tif\n- ExperimentID: Unique identifier for the experiment.\n- AcquisitionDate: Date of image acquisition (YYMMDD).\n- Microscope: Name of the microscope used for acquisition.\n-- JEM1400: Jeol JEM-1400 Flash TEM\n- SampleType: Describes the grid and section.\n-- Slot{GridBoxPosition}{Grid}{Section}: e.g., Slot812 indicates Grid Box Position 8, Grid 1, Section 2.\n- PixelSize: Resolution of the image.\n-- xy{Value}nm: For 2D images, e.g., xy340nm for a pixel size of 340 nm.\n\nExamples:\nSection TEM map: 266_221116_JEM1400_Slot812_xy340nm.tif\nROI TEM map: 266_240222_JEM1400_Slot812_xy3.4nm.tif\nTEM Tomography: 266_240515_JEM1400_Slot813_xy1.8nm.tif\nTEM Tomography: 266_240530_JEM1400_Slot733_xy1.8nm.tif\n\nFilename and description\nEM2B6/266_221116_JEM1400_Slot812_xy170nm.tif                               \"Section TEM map for Fig.5A\"\nEM2B6/266_240326GN_JEM1400_Slot812_xy3.4nm_img.zarr                        \"ROI TEM map for Figs.5D and 5E\"\nEM2B6/266_240515_JEM1400_Slot813_xy1.8nm.tif                               \"TEM tomogram for Fig.5\"\nEM2B6/266_240515_JEM1400_Slot813_xy3.4nm_z45_img.tif                       \"TEM tomogram for Fig.5F-ii\"\nEM2B6/266_240530_JEM1400_Slot733_xy3.4nm_x33_y0_z43-60.tif                 \"TEM tomogram for Fig.5F-i\"\nEM2B6/266_240530_JEM1400_Slot733_xy3.4nm_x33_y0_z53_img.tif                \"TEM tomogram for Fig.5F-i\"\nEM2B6/266_240530_JEM1400_Slot733_xy3.4nm_x33_y0_z53_seg.tif                \"TEM tomogram for Fig.5F-i\"\nEM2B6/266_240530_JEM1400_Slot733_xy1.8nm.tif                               \"TEM tomogram for Fig.5\"\nEM2B6/266_240621GN_JEM1400_Slot721_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot722_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot723_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot731_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot732_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot733_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot734_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot812_xy136nm_x187_y294_img.tif               \"Section TEM map - cell and nuclei segmentation for Fig.5D\"\nEM2B6/266_240621GN_JEM1400_Slot812_xy136nm_x187_y294_labels.tif            \"Section TEM map - cell and nuclei segmentation for Fig.5D\"\nEM2B6/266_240621GN_JEM1400_Slot812_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot813_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot814_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot821_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot822_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot823_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"\nEM2B6/266_240621GN_JEM1400_Slot824_xy136nm_x187_y294_seg.tif               \"Section TEM map - nuclei segmentation for Fig.5B\"","image_width":null,"image_height":null}],"workflow_file":null,"grant_references":[{"funding_body":"Wellcome Trust","code":"215508/Z/19/Z","country":"United Kingdom"},{"funding_body":"Biotechnology and Biological Sciences Research Council (BBSRC)","code":"BB/Z514962/1","country":"United Kingdom"},{"funding_body":"Royal Society","code":"INF\\R2\\202061","country":"United Kingdom"}],"version_history":[],"title":"Benchmark TEM data of mouse brain previously imaged by Nikon confocal microscopy","principal_investigator":[{"author_orcid":null,"middle_name":null,"organization":"Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London","street":"Great Maze Pond","town_or_city":"London","state_or_province":null,"post_or_zip":"SE1 1UL","telephone":null,"fax":null,"first_name":"Kohki","last_name":"Konishi","email":"kohki.konishi [at] kcl.ac.uk","country":"United Kingdom","entry":"EMPIAR-12850"},{"author_orcid":"0009-0002-1572-598X","middle_name":null,"organization":"Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London","street":"Great Maze Pond","town_or_city":"London","state_or_province":null,"post_or_zip":"SE1 1UL","telephone":null,"fax":null,"first_name":"Kohki","last_name":"Konishi","email":"kohki.konishi [at] kcl.ac.uk","country":"United Kingdom","entry":"EMPIAR-12850"},{"author_orcid":"0000-0003-1542-6218","middle_name":null,"organization":"Centre for Ultrastructural Imaging, King’s College London, London, UK","street":"Great Maze Pond","town_or_city":"London","state_or_province":null,"post_or_zip":"SE1 1UL","telephone":null,"fax":null,"first_name":"Roland","last_name":"Fleck","email":"roland.fleck [at] kcl.ac.uk","country":"United Kingdom","entry":"EMPIAR-12850"}],"status":"REL","deposition_date":"2025-06-16","release_date":"2025-09-05","obsolete_date":null,"update_date":"2025-09-05","corresponding_author":{"author":{"author_orcid":"0009-0002-1572-598X","middle_name":null,"organization":"Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London","street":"Great Maze Pond","town_or_city":"London","state_or_province":null,"post_or_zip":"SE1 1UL","first_name":"Kohki","last_name":"Konishi","country":"United Kingdom"}},"authors":[{"author":{"name":"Konishi KK","author_orcid":"0009-0002-1572-598X"}},{"author":{"name":"Neves GN","author_orcid":"0000-0001-6463-6997"}},{"author":{"name":"Russell MR","author_orcid":"0000-0003-4608-7669"}},{"author":{"name":"Burrone JB","author_orcid":"0000-0003-1233-668X"}},{"author":{"name":"Fleck RF","author_orcid":"0000-0003-1542-6218"}}],"cross_references":[],"biostudies_references":[{"name":"S-BIAD2077"}],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Konishi KK","author_orcid":"0009-0002-1572-598X"},{"name":"Neves GN","author_orcid":"0000-0001-6463-6997"},{"name":"Russell MR","author_orcid":"0000-0003-4608-7669"},{"name":"Mimura MM","author_orcid":null},{"name":"Burrone JB","author_orcid":"0000-0003-1233-668X"},{"name":"Fleck RF","author_orcid":"0000-0003-1542-6218"}],"editors":[],"published":false,"j_or_nj_citation":true,"title":"A workflow for semi-automated volume correlative light microscopy and transmission electron tomography","volume":null,"country":"United Kingdom","first_page":null,"last_page":null,"year":null,"language":null,"doi":"10.1111/jmi.13436","pubmedid":null,"details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Journal of Microscopy","journal_abbreviation":"J. Microsc","issue":null,"preprint":true}],"dataset_size":"2.5 GB","experiment_type":"CLEM","scale":"tissue","entry_doi":"10.6019/EMPIAR-12850"}}