SyMBac
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Introduction
Introduction
Installation
FAQs
Guide: Mother Machine
Mother machine simulations
Guide: Agar Pad
Agar pad simulations
Examples
Convert SyMBac data to be compatible with Omnipose
Training Omnipose
Segmenting with Omnipose
Classes reference
SyMBac.cell
SyMBac.PSF
SyMBac.renderer
SyMBac.simulation
API reference
SyMBac.cell_geometry
SyMBac.cell_simulation
SyMBac.drawing
SyMBac.misc
SyMBac.pySHINE
SyMBac
Index
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Index
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C
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D
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F
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G
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I
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L
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M
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O
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P
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R
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S
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U
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V
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W
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__init__() (SyMBac.cell.Cell method)
(SyMBac.PSF.Camera method)
(SyMBac.PSF.PSF_generator method)
(SyMBac.renderer.Renderer method)
(SyMBac.simulation.Simulation method)
C
Camera (class in SyMBac.PSF)
Cell (class in SyMBac.cell)
centroid() (in module SyMBac.cell_geometry)
create_pm_cell() (SyMBac.cell.Cell method)
create_space() (in module SyMBac.cell_simulation)
D
draw_scene() (in module SyMBac.drawing)
F
find_farthest_vertices() (in module SyMBac.drawing)
G
gaussian_2D() (SyMBac.PSF.PSF_generator static method)
gen_cell_props_for_draw() (in module SyMBac.drawing)
generate_curve_props() (in module SyMBac.drawing)
generate_PC_OPL() (SyMBac.renderer.Renderer method)
generate_test_comparison() (SyMBac.renderer.Renderer method)
generate_training_data() (SyMBac.renderer.Renderer method)
get_angle() (SyMBac.cell.Cell method)
get_centroid() (in module SyMBac.drawing)
(SyMBac.cell.Cell method)
get_condensers() (SyMBac.PSF.PSF_generator static method)
get_distance() (in module SyMBac.drawing)
get_fluorescence_kernel() (SyMBac.PSF.PSF_generator static method)
get_midpoint() (in module SyMBac.drawing)
get_phase_contrast_kernel() (SyMBac.PSF.PSF_generator static method)
get_sample_images() (in module SyMBac.misc)
get_space_size() (in module SyMBac.drawing)
get_vertex_list() (SyMBac.cell.Cell method)
get_vertices() (in module SyMBac.cell_geometry)
I
is_dividing() (SyMBac.cell.Cell method)
L
lumMatch() (in module SyMBac.pySHINE)
M
make_images_same_shape() (in module SyMBac.drawing)
midpoint_intercept() (in module SyMBac.drawing)
module
SyMBac.cell_geometry
SyMBac.cell_simulation
SyMBac.drawing
SyMBac.misc
SyMBac.pySHINE
O
OPL_to_FL() (in module SyMBac.drawing)
optimise_synth_image() (SyMBac.renderer.Renderer method)
P
place_cell() (in module SyMBac.drawing)
PSF_generator (class in SyMBac.PSF)
R
raster_cell() (in module SyMBac.drawing)
render_dark_image() (SyMBac.PSF.Camera method)
Renderer (class in SyMBac.renderer)
rescale_shine() (in module SyMBac.pySHINE)
resize_mask() (in module SyMBac.misc)
rotate() (in module SyMBac.cell_geometry)
run_simulation() (in module SyMBac.cell_simulation)
(SyMBac.simulation.Simulation method)
S
sfMatch() (in module SyMBac.pySHINE)
Simulation (class in SyMBac.simulation)
somb() (SyMBac.PSF.PSF_generator static method)
step_and_update() (in module SyMBac.cell_simulation)
SyMBac.cell_geometry
module
SyMBac.cell_simulation
module
SyMBac.drawing
module
SyMBac.misc
module
SyMBac.pySHINE
module
U
unet_weight_map() (in module SyMBac.misc)
update_cell_lengths() (in module SyMBac.cell_simulation)
update_cell_parents() (in module SyMBac.cell_simulation)
update_cell_positions() (in module SyMBac.cell_simulation)
update_length() (SyMBac.cell.Cell method)
update_parent() (SyMBac.cell.Cell method)
update_pm_cells() (in module SyMBac.cell_simulation)
update_position() (SyMBac.cell.Cell method)
V
vertices_slope() (in module SyMBac.drawing)
visualise_in_napari() (SyMBac.simulation.Simulation method)
W
wall() (in module SyMBac.cell_geometry)
wipe_space() (in module SyMBac.cell_simulation)
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