| haadf_projection_export: |
| source: "50-frame HAADF series in each Velox EMD" |
| source_shape_per_tilt: [400, 300, 50] |
| source_dtype: uint16 |
| output: derived/haadf/HAADF_stack.tif |
| frame_selection: UNKNOWN |
| rejected_frames: UNKNOWN |
| combination: UNKNOWN |
| drift_correction: UNKNOWN |
| normalization: UNKNOWN |
| crop: UNKNOWN |
| binning: UNKNOWN |
|
|
| haadf_alignment: |
| input: derived/haadf/HAADF_stack.tif |
| output: derived/haadf/HAADF_aligned.tiff |
| parameters: derived/haadf/alignment/ali_haadf.json |
| reference_angle_deg: 0 |
| parameter_count: 16 |
| parameter_shape: [16, 2] |
| parameter_units: pixels |
| parameter_meaning: "translation used to align each HAADF projection to the 0-degree acquisition" |
| zero_degree_entry: [0, 0] |
| component_order: UNKNOWN |
| sign_convention: UNKNOWN |
| interpolation: UNKNOWN |
| boundary_handling: UNKNOWN |
|
|
| eds_map_extraction: |
| source: "50-frame EDS spectrum stream in each Velox EMD" |
| detector: "Super-X, four SDDs" |
| map_mode: NetIntensity |
| lines: |
| Ge: "Kα" |
| Te: "Lα" |
| Sb: "Lα" |
| Ti: "Kα" |
| embedded_additional_elements: [N, O, Si] |
| rendered_map_filter: |
| enabled: true |
| type: Mean |
| kernel_size: 3 |
| spectral_filter: |
| enabled: false |
| type: Gaussian |
| absorption_correction: |
| enabled: false |
|
|
| publication_elemental_alignment: |
| software: Fiji |
| plugin: MultiStackReg |
| transform: translation-only |
| reference_channel_for_transform_estimation: Ge |
| applied_to_channels: [Ge, Te, Sb, Ti] |
| later_output_shape: [176, 112] |
| binning_factor: 2 |
| normalization: "independent maximum normalization per channel" |
| note: "The distributed 400x300 TIFFs precede this later reconstruction preprocessing." |
|
|
