Index

A

add_samples() (in module fibsem.sample)

adorned_image() (in module fibsem.data) all_roi_coordinates() (in module fibsem.milling)

C

centroid() (in module fibsem.orientation)

configure_parser() (in module fibsem.user_input) create_milling_patterns() (in module fibsem.autoscript)

D

display_crosshairs() (fibsem.sample.Embryo method) display_milling_axes() (fibsem.sample.Embryo method) display_milling_rois() (fibsem.sample.Embryo method) display_milling_rois_mask() (fibsem.sample.Embryo method)

draw_crosshairs() (in module fibsem.display) draw_milling_axes() (in module fibsem.display) draw_object_axes() (in module fibsem.display) draw_rotated_rects() (in module fibsem.display)

E

Embryo (class in fibsem.sample) embryo() (in module fibsem.data)

embryo_adorned() (in module fibsem.data) embryo_mask() (in module fibsem.data) embryo_mask_adorned() (in module fibsem.data)

F

fibsem (module) fibsem.autoscript (module) fibsem.conversions (module) fibsem.data (module) fibsem.display (module) fibsem.main (module)

fibsem.milling (module) fibsem.mocktypes (module) fibsem.orientation (module) fibsem.sample (module) fibsem.segmentation (module) fibsem.segmentation.manual_segmentation (module) fibsem.user_input (module)

I

image_data (fibsem.mocktypes.MockAdornedImage attribute)

initialize() (in module fibsem.autoscript)

L

line_length() (in module fibsem.orientation)

load_config() (in module fibsem.user_input) load_image() (in module fibsem.data)

M

major_minor_axes_pixels() (in module fibsem.orientation) major_minor_axes_realspace() (in module fibsem.orientation) manual_segmentation() (in module fibsem.segmentation.manual_segmentation) meters_to_pixels() (in module fibsem.conversions) mill_all_samples() (in module fibsem.milling) mill_single_sample() (in module fibsem.milling)

mock_user_settings() (in module fibsem.mocktypes) MockAdornedImage (class in fibsem.mocktypes) MockBinaryResult (class in fibsem.mocktypes) MockMetadata (class in fibsem.mocktypes) MockPixelSize (class in fibsem.mocktypes) move_to_stage_position() (fibsem.sample.Sample method) multi_axis() (in module fibsem.orientation)

O

orientation() (fibsem.sample.Embryo method)

P

patterning_engine() (in module fibsem.autoscript) pixels_to_meters() (in module fibsem.conversions)

pixelsize_x (fibsem.mocktypes.MockAdornedImage attribute) pixelsize_y (fibsem.mocktypes.MockAdornedImage attribute) print_vars() (fibsem.sample.Sample method)

Q

quick_plot() (in module fibsem.display)

R

reset_patterning_state() (in module fibsem.autoscript) response() (in module fibsem.user_input)

rotation_angle() (in module fibsem.orientation) run_milling() (in module fibsem.main)

S

Sample (class in fibsem.sample) save_vars() (fibsem.sample.Sample method) select_point() (in module fibsem.segmentation.manual_segmentation) set_axes_for_milling() (fibsem.sample.Embryo method) set_head_position() (fibsem.sample.Embryo method) set_image() (fibsem.sample.Sample method)

set_imagedata() (fibsem.mocktypes.MockAdornedImage method) set_mask() (fibsem.sample.Sample method) set_milling_rois() (fibsem.sample.Embryo method) set_pixel_size() (fibsem.sample.Sample method) set_pixelsize() (fibsem.mocktypes.MockAdornedImage method) (fibsem.mocktypes.MockPixelSize method) set_stage_position() (fibsem.sample.Sample method)