micrographs - single frame

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TEM Imaging and Data Acquisition

Section TEM Mapping
Entire 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).

Region of Interest (ROI) TEM Mapping
High-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).

TEM Tomography
For 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.

File Naming Convention
Files are named according to the following structure:
{ExperimentID}_{AcquisitionDate}_{Microscope}_{SampleType}_{PixelSize}.tif
- ExperimentID: Unique identifier for the experiment.
- AcquisitionDate: Date of image acquisition (YYMMDD).
- Microscope: Name of the microscope used for acquisition.
-- JEM1400: Jeol JEM-1400 Flash TEM
- SampleType: Describes the grid and section.
-- Slot{GridBoxPosition}{Grid}{Section}: e.g., Slot812 indicates Grid Box Position 8, Grid 1, Section 2.
- PixelSize: Resolution of the image.
-- xy{Value}nm: For 2D images, e.g., xy340nm for a pixel size of 340 nm.

Examples:
Section TEM map: 266_221116_JEM1400_Slot812_xy340nm.tif
ROI TEM map: 266_240222_JEM1400_Slot812_xy3.4nm.tif
TEM Tomography: 266_240515_JEM1400_Slot813_xy1.8nm.tif
TEM Tomography: 266_240530_JEM1400_Slot733_xy1.8nm.tif

Filename and description
EM2B6/266_221116_JEM1400_Slot812_xy170nm.tif "Section TEM map for Fig.5A"
EM2B6/266_240326GN_JEM1400_Slot812_xy3.4nm_img.zarr "ROI TEM map for Figs.5D and 5E"
EM2B6/266_240515_JEM1400_Slot813_xy1.8nm.tif "TEM tomogram for Fig.5"
EM2B6/266_240515_JEM1400_Slot813_xy3.4nm_z45_img.tif "TEM tomogram for Fig.5F-ii"
EM2B6/266_240530_JEM1400_Slot733_xy3.4nm_x33_y0_z43-60.tif "TEM tomogram for Fig.5F-i"
EM2B6/266_240530_JEM1400_Slot733_xy3.4nm_x33_y0_z53_img.tif "TEM tomogram for Fig.5F-i"
EM2B6/266_240530_JEM1400_Slot733_xy3.4nm_x33_y0_z53_seg.tif "TEM tomogram for Fig.5F-i"
EM2B6/266_240530_JEM1400_Slot733_xy1.8nm.tif "TEM tomogram for Fig.5"
EM2B6/266_240621GN_JEM1400_Slot721_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot722_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot723_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot731_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot732_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot733_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot734_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot812_xy136nm_x187_y294_img.tif "Section TEM map - cell and nuclei segmentation for Fig.5D"
EM2B6/266_240621GN_JEM1400_Slot812_xy136nm_x187_y294_labels.tif "Section TEM map - cell and nuclei segmentation for Fig.5D"
EM2B6/266_240621GN_JEM1400_Slot812_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot813_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot814_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot821_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot822_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot823_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"
EM2B6/266_240621GN_JEM1400_Slot824_xy136nm_x187_y294_seg.tif "Section TEM map - nuclei segmentation for Fig.5B"

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