big-fish
stable
Preprocessing
I/O operations
Image preparation
Augmentation
Spot detection
Automated spot detection
Dense regions decomposition
Subpixel fitting
Cluster detection
Colocalization
Segmentation
Nucleus segmentation
Cell segmentation
Postprocessing
Analysis
Single-cell identification
Features engineering
Visualization
Field of view plot
Detection plot
Segmentation plot
Single-cell plot
Utils
Utility functions
big-fish
Index
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Index
A
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B
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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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I
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L
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M
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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
A
apply_unet_3_classes() (in module bigfish.segmentation)
apply_unet_distance_double() (in module bigfish.segmentation)
apply_watershed() (in module bigfish.segmentation)
augment_2d() (in module bigfish.stack)
augment_2d_function() (in module bigfish.stack)
augment_8_times() (in module bigfish.stack)
augment_8_times_reversed() (in module bigfish.stack)
automated_threshold_setting() (in module bigfish.detection)
B
build_reference_spot() (in module bigfish.detection)
C
cast_img_float32() (in module bigfish.stack)
cast_img_float64() (in module bigfish.stack)
cast_img_uint16() (in module bigfish.stack)
cast_img_uint8() (in module bigfish.stack)
cell_watershed() (in module bigfish.segmentation)
center_mask_coord() (in module bigfish.multistack)
centered_moving_average() (in module bigfish.stack)
check_array() (in module bigfish.stack)
check_df() (in module bigfish.stack)
check_hash() (in module bigfish.stack)
check_input_data() (in module bigfish.stack)
check_parameter() (in module bigfish.stack)
check_range_value() (in module bigfish.stack)
clean_segmentation() (in module bigfish.segmentation)
complete_coord_boundaries() (in module bigfish.multistack)
compute_features() (in module bigfish.classification)
compute_focus() (in module bigfish.stack)
compute_hash() (in module bigfish.stack)
compute_image_standardization() (in module bigfish.stack)
compute_mean_convexity_ratio() (in module bigfish.segmentation)
compute_mean_diameter() (in module bigfish.segmentation)
compute_snr_spots() (in module bigfish.detection)
compute_surface_ratio() (in module bigfish.segmentation)
convert_spot_coordinates() (in module bigfish.detection)
count_instances() (in module bigfish.segmentation)
create_colormap() (in module bigfish.plot)
D
decompose_dense() (in module bigfish.detection)
detect_clusters() (in module bigfish.detection)
detect_spots() (in module bigfish.detection)
detect_spots_colocalization() (in module bigfish.multistack)
dilation_filter() (in module bigfish.stack)
E
erosion_filter() (in module bigfish.stack)
extract_cell() (in module bigfish.multistack)
extract_spots_from_frame() (in module bigfish.multistack)
F
features_area() (in module bigfish.classification)
features_centrosome() (in module bigfish.classification)
features_dispersion() (in module bigfish.classification)
features_distance() (in module bigfish.classification)
features_foci() (in module bigfish.classification)
features_in_out_nucleus() (in module bigfish.classification)
features_protrusion() (in module bigfish.classification)
features_topography() (in module bigfish.classification)
fit_subpixel() (in module bigfish.detection)
focus_projection() (in module bigfish.stack)
from_3_classes_to_instances() (in module bigfish.segmentation)
from_binary_to_coord() (in module bigfish.multistack)
from_boundaries_to_surface() (in module bigfish.multistack)
from_coord_to_frame() (in module bigfish.multistack)
from_coord_to_surface() (in module bigfish.multistack)
from_distance_to_instances() (in module bigfish.segmentation)
from_surface_to_boundaries() (in module bigfish.multistack)
G
gaussian_2d() (in module bigfish.detection)
gaussian_3d() (in module bigfish.detection)
gaussian_filter() (in module bigfish.stack)
get_breaking_point() (in module bigfish.detection)
get_dense_region() (in module bigfish.detection)
get_elbow_value_colocalized() (in module bigfish.multistack)
get_elbow_values() (in module bigfish.detection)
get_eps_float32() (in module bigfish.stack)
get_features_name() (in module bigfish.classification)
get_in_focus_indices() (in module bigfish.stack)
get_marge_padding() (in module bigfish.stack)
get_margin_value() (in module bigfish.stack)
get_minmax_values() (in module bigfish.plot)
get_object_radius_nm() (in module bigfish.detection)
get_object_radius_pixel() (in module bigfish.detection)
get_spot_surface() (in module bigfish.detection)
get_spot_volume() (in module bigfish.detection)
get_watershed_relief() (in module bigfish.segmentation)
I
identify_objects_in_region() (in module bigfish.multistack)
in_focus_selection() (in module bigfish.stack)
initialize_grid() (in module bigfish.detection)
L
label_instances() (in module bigfish.segmentation)
load_and_save_url() (in module bigfish.stack)
local_maximum_detection() (in module bigfish.detection)
log_filter() (in module bigfish.stack)
M
match_nuc_cell() (in module bigfish.multistack)
maximum_filter() (in module bigfish.stack)
maximum_projection() (in module bigfish.stack)
mean_filter() (in module bigfish.stack)
mean_projection() (in module bigfish.stack)
median_filter() (in module bigfish.stack)
median_projection() (in module bigfish.stack)
merge_labels() (in module bigfish.segmentation)
minimum_filter() (in module bigfish.stack)
modelize_spot() (in module bigfish.detection)
moving_average() (in module bigfish.stack)
P
plot_cell() (in module bigfish.plot)
plot_cell_coordinates() (in module bigfish.plot)
plot_detection() (in module bigfish.plot)
plot_elbow() (in module bigfish.plot)
plot_elbow_colocalized() (in module bigfish.plot)
plot_images() (in module bigfish.plot)
plot_reference_spot() (in module bigfish.plot)
plot_segmentation() (in module bigfish.plot)
plot_segmentation_boundary() (in module bigfish.plot)
plot_segmentation_diff() (in module bigfish.plot)
plot_sharpness() (in module bigfish.plot)
plot_yx() (in module bigfish.plot)
precompute_erf() (in module bigfish.detection)
prepare_extracted_data() (in module bigfish.classification)
R
read_array() (in module bigfish.stack)
read_array_from_csv() (in module bigfish.stack)
read_cell_extracted() (in module bigfish.stack)
read_dataframe_from_csv() (in module bigfish.stack)
read_dv() (in module bigfish.stack)
read_image() (in module bigfish.stack)
read_uncompressed() (in module bigfish.stack)
remove_background_gaussian() (in module bigfish.stack)
remove_background_mean() (in module bigfish.stack)
remove_disjoint() (in module bigfish.segmentation)
remove_segmented_nuc() (in module bigfish.segmentation)
remove_transcription_site() (in module bigfish.multistack)
rescale() (in module bigfish.stack)
resize_image() (in module bigfish.stack)
S
save_array() (in module bigfish.stack)
save_cell_extracted() (in module bigfish.stack)
save_data_to_csv() (in module bigfish.stack)
save_image() (in module bigfish.stack)
save_plot() (in module bigfish.plot)
simulate_gaussian_mixture() (in module bigfish.detection)
spots_thresholding() (in module bigfish.detection)
summarize_extraction_results() (in module bigfish.multistack)
T
thresholding() (in module bigfish.segmentation)
U
unet_3_classes_nuc() (in module bigfish.segmentation)
unet_distance_edge_double() (in module bigfish.segmentation)
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