DLITE
latest
Contents:
Overview and install
Usage
Generate_Voronoi_data.ipynb
Demo_notebook_SurfaceEvolver.ipynb
Demo_notebook_ZO-1.ipynb
Compare_CELLFIT_DLITE.ipynb
FOV_drift.ipynb
Example
A minimal example of how to use DLITE
A bit about the data structure
Physics
Tension balance
Pressure balance
Synthetic Data
Generate Voronoi colony mesh
Converting a colony mesh to a mesh suitable for use with SurfaceEvolver
Convert SurfaceEvolver mesh to force network
Compare imputed force network between CellFIT and DLITE
Simulate FOV drift in a single colony
ZO-1 Data
ZO-1 mesh to force network
Package modules
DLITE package
Submodules
DLITE.AICS_data module
DLITE.Lloyd_relaxation_class module
DLITE.ManualTracing module
DLITE.ManualTracingMultiple module
DLITE.PlottingFunctions module
DLITE.SaveSurfEvolFile module
DLITE.SurfaceEvolver module
DLITE.cell_describe module
Module contents
Credits
Development Lead
Contributors
DLITE
Docs
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Index
Edit on GitHub
Index
A
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
A
add_cell() (DLITE.cell_describe.colony method)
add_edge() (DLITE.AICS_data.data method)
add_gogo3() (DLITE.SaveSurfEvolFile.SaveFile method)
add_node() (DLITE.AICS_data.data method)
all_perims_areas_lengths() (DLITE.PlottingFunctions.PlottingFunctions method)
all_tensions_and_radius_and_pressures() (DLITE.PlottingFunctions.PlottingFunctions method)
alternative_computation_based_on_prev() (DLITE.ManualTracingMultiple.ManualTracingMultiple method)
arc_translation() (DLITE.cell_describe.edge method)
area() (DLITE.cell_describe.cell method)
assign_intial_guesses() (DLITE.ManualTracingMultiple.ManualTracingMultiple method)
(DLITE.SurfaceEvolver.SurfaceEvolver method)
Atlas (class in DLITE.Lloyd_relaxation_class)
C
calculate_pressure() (DLITE.cell_describe.colony method)
calculate_tension() (DLITE.cell_describe.colony method)
cell (class in DLITE.cell_describe)
cell_coefficients (DLITE.cell_describe.edge attribute)
cell_indices (DLITE.cell_describe.edge attribute)
cell_rhs (DLITE.cell_describe.edge attribute)
cells (DLITE.cell_describe.edge attribute)
center_of_circle (DLITE.cell_describe.edge attribute)
centroid() (DLITE.cell_describe.cell method)
check_repeat_labels() (DLITE.PlottingFunctions.PlottingFunctions method)
cleanup() (DLITE.ManualTracing.ManualTracing method)
co_ordinates (DLITE.cell_describe.edge attribute)
co_ordinates() (DLITE.ManualTracing.ManualTracing method)
colony (class in DLITE.cell_describe)
colony_cell (DLITE.cell_describe.cell attribute)
computation_based_on_prev_surface_evolver() (DLITE.SurfaceEvolver.SurfaceEvolver method)
compute() (DLITE.AICS_data.data method)
(DLITE.SurfaceEvolver.SurfaceEvolver method)
connected_edges (DLITE.cell_describe.edge attribute)
convex_concave() (DLITE.cell_describe.edge method)
curve_fit_residual (DLITE.cell_describe.edge attribute)
D
data (class in DLITE.AICS_data)
dictionary (DLITE.cell_describe.colony attribute)
DLITE (module)
DLITE.AICS_data (module)
DLITE.cell_describe (module)
DLITE.Lloyd_relaxation_class (module)
DLITE.ManualTracing (module)
DLITE.ManualTracingMultiple (module)
DLITE.PlottingFunctions (module)
DLITE.SaveSurfEvolFile (module)
DLITE.SurfaceEvolver (module)
E
edge (class in DLITE.cell_describe)
edge_angle() (DLITE.cell_describe.edge method)
edge_indices (DLITE.cell_describe.node attribute)
edges (DLITE.cell_describe.colony attribute)
(DLITE.cell_describe.node attribute)
equality_constraint_pressure() (DLITE.cell_describe.colony method)
equality_constraint_tension() (DLITE.cell_describe.colony method)
F
find_cycles() (DLITE.AICS_data.data static method)
first_computation() (DLITE.ManualTracingMultiple.ManualTracingMultiple method)
(DLITE.SurfaceEvolver.SurfaceEvolver method)
fit() (DLITE.AICS_data.data method)
fit_X_Y() (DLITE.ManualTracing.ManualTracing method)
FOV_Drift() (DLITE.SurfaceEvolver.SurfaceEvolver method)
G
generate_voronoi() (DLITE.Lloyd_relaxation_class.Atlas method)
get_adjacent_pressures() (DLITE.cell_describe.colony method)
get_FOV() (DLITE.SurfaceEvolver.SurfaceEvolver static method)
get_min_max_by_outliers_iqr() (DLITE.PlottingFunctions.PlottingFunctions method)
get_module_version() (in module DLITE)
get_nodes_edges_cells() (DLITE.ManualTracingMultiple.ManualTracingMultiple method)
get_repeat_cell() (DLITE.PlottingFunctions.PlottingFunctions method)
get_repeat_edge() (DLITE.PlottingFunctions.PlottingFunctions method)
get_repeat_nodes() (DLITE.PlottingFunctions.PlottingFunctions method)
get_x_y_data() (DLITE.ManualTracingMultiple.ManualTracingMultiple method)
get_X_Y_data_only_junction() (DLITE.SurfaceEvolver.SurfaceEvolver method)
ground_truth (DLITE.cell_describe.edge attribute)
ground_truth_pressure (DLITE.cell_describe.cell attribute)
guess_pressure (DLITE.cell_describe.cell attribute)
guess_tension (DLITE.cell_describe.edge attribute)
H
horizontal_vectors (DLITE.cell_describe.node attribute)
I
initial_conditions() (DLITE.cell_describe.colony method)
initial_numbering() (DLITE.ManualTracingMultiple.ManualTracingMultiple method)
(DLITE.SurfaceEvolver.SurfaceEvolver method)
K
kill_edge() (DLITE.cell_describe.edge method)
L
label (DLITE.cell_describe.cell attribute)
(DLITE.cell_describe.edge attribute)
(DLITE.cell_describe.node attribute)
label_cells() (DLITE.ManualTracingMultiple.ManualTracingMultiple method)
(DLITE.SurfaceEvolver.SurfaceEvolver method)
M
main_computation_based_on_prev() (DLITE.ManualTracingMultiple.ManualTracingMultiple method)
make_bounds() (DLITE.cell_describe.colony method)
make_pressure_matrix() (DLITE.cell_describe.colony method)
make_tension_matrix() (DLITE.cell_describe.colony method)
ManualTracing (class in DLITE.ManualTracing)
ManualTracingMultiple (class in DLITE.ManualTracingMultiple)
N
node (class in DLITE.cell_describe)
nodes (DLITE.cell_describe.colony attribute)
(DLITE.cell_describe.edge attribute)
O
objective_function_pressure() (DLITE.cell_describe.colony method)
objective_function_tension() (DLITE.cell_describe.colony method)
outliers_modified_z_score() (DLITE.PlottingFunctions.PlottingFunctions method)
P
perimeter() (DLITE.cell_describe.cell method)
plot() (DLITE.AICS_data.data method)
(DLITE.cell_describe.cell method)
(DLITE.cell_describe.colony method)
(DLITE.cell_describe.edge method)
(DLITE.cell_describe.node method)
plot_abnormal_edges() (DLITE.PlottingFunctions.PlottingFunctions method)
plot_both_tension_pressure() (DLITE.PlottingFunctions.PlottingFunctions method)
plot_compare_single_edge_tension() (DLITE.PlottingFunctions.PlottingFunctions method)
plot_fill() (DLITE.cell_describe.edge method)
plot_guess_pressures() (DLITE.PlottingFunctions.PlottingFunctions method)
plot_guess_tension() (DLITE.PlottingFunctions.PlottingFunctions method)
plot_histogram() (DLITE.PlottingFunctions.PlottingFunctions method)
plot_pressures() (DLITE.cell_describe.colony method)
(DLITE.PlottingFunctions.PlottingFunctions method)
plot_single_cells() (DLITE.PlottingFunctions.PlottingFunctions method)
plot_single_edges() (DLITE.PlottingFunctions.PlottingFunctions method)
plot_single_nodes() (DLITE.PlottingFunctions.PlottingFunctions method)
plot_tensions() (DLITE.cell_describe.colony method)
(DLITE.PlottingFunctions.PlottingFunctions method)
plot_tensor_dataframe() (DLITE.PlottingFunctions.PlottingFunctions method)
PlottingFunctions (class in DLITE.PlottingFunctions)
post_processing() (DLITE.AICS_data.data method)
pressure (DLITE.cell_describe.cell attribute)
pressure_matrix (DLITE.cell_describe.colony attribute)
pressure_rhs (DLITE.cell_describe.colony attribute)
previous_label (DLITE.cell_describe.edge attribute)
(DLITE.cell_describe.node attribute)
previous_tension_vectors (DLITE.cell_describe.node attribute)
R
recursive_cycle_finder() (DLITE.cell_describe.edge method)
relax_points() (DLITE.Lloyd_relaxation_class.Atlas method)
remove_dangling_edges() (DLITE.AICS_data.data method)
remove_edge() (DLITE.cell_describe.node method)
remove_outliers() (DLITE.cell_describe.colony method)
remove_small_cells() (DLITE.AICS_data.data method)
remove_two_edge_connections() (DLITE.AICS_data.data method)
residual_vector (DLITE.cell_describe.node attribute)
S
save() (DLITE.SaveSurfEvolFile.SaveFile method)
SaveFile (class in DLITE.SaveSurfEvolFile)
scipy_opt_minimze() (DLITE.cell_describe.colony method)
seaborn_cells_dataframe_tensor() (DLITE.PlottingFunctions.PlottingFunctions method)
seaborn_nodes_dataframe() (DLITE.PlottingFunctions.PlottingFunctions method)
seaborn_plot() (DLITE.PlottingFunctions.PlottingFunctions method)
single_edge_plotting() (DLITE.PlottingFunctions.PlottingFunctions method)
solve_constrained_lsq() (DLITE.cell_describe.colony static method)
straight_length (DLITE.cell_describe.edge attribute)
SurfaceEvolver (class in DLITE.SurfaceEvolver)
T
tension (DLITE.cell_describe.edge attribute)
tension_matrix (DLITE.cell_describe.colony attribute)
tension_vectors (DLITE.cell_describe.node attribute)
track_timestep() (DLITE.ManualTracingMultiple.ManualTracingMultiple method)
(DLITE.SurfaceEvolver.SurfaceEvolver method)
U
unit_vectors() (DLITE.cell_describe.edge method)
V
velocity_vector (DLITE.cell_describe.node attribute)
vertical_vectors (DLITE.cell_describe.node attribute)
W
which_cell() (DLITE.cell_describe.edge method)
X
x (DLITE.cell_describe.node attribute)
x() (DLITE.AICS_data.data method)
Y
y (DLITE.cell_describe.node attribute)
y() (DLITE.AICS_data.data method)