Index

A

analyze_graph() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method)

as_napari_rectangle() (microglia_analyzer.tiles.patch.Patch2D method) as_tsv() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method)

B

bindings_as_napari_shapes() (in module microglia_analyzer.utils)

bindings_from_yolo() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method) bindings_to_yolo() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method)

C

calculate_iou() (in module microglia_analyzer.utils) classify_microglia() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method) compute_connected_components_penalty() (in module microglia_analyzer.custom_loss)

compute_skeleton_reward() (in module microglia_analyzer.custom_loss) convert_hex_colors_to_bgr() (in module microglia_analyzer.utils) custom_loss() (in module microglia_analyzer.custom_loss)

D

dice_loss_function() (in module microglia_analyzer.custom_loss)

download_from_web() (in module microglia_analyzer.utils) draw_bounding_boxes() (in module microglia_analyzer.utils)

F

finished (microglia_analyzer.qt_workers.QtBatchRunners attribute) (microglia_analyzer.qt_workers.QtClassifyMicroglia attribute) (microglia_analyzer.qt_workers.QtMeasureMicroglia attribute) (microglia_analyzer.qt_workers.QtSegmentMicroglia attribute)

G

generate_random_bindings() (in module microglia_analyzer.utils) get_all_tiff_files() (in module microglia_analyzer.utils) get_classification_version() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method)

get_grid_size() (microglia_analyzer.tiles.tiler.ImageTiler2D method) get_layout() (microglia_analyzer.tiles.tiler.ImageTiler2D method) get_mask() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method) get_segmentation_version() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method)

H

hex_to_bgr() (in module microglia_analyzer.utils)

I

image_to_tiles() (microglia_analyzer.tiles.tiler.ImageTiler2D method) ImageTiler2D (class in microglia_analyzer.tiles.tiler)

inference() (microglia_analyzer.unet_worker.UNetWorker method) interupt() (microglia_analyzer.qt_workers.QtBatchRunners method)

M

make_gradient_patch() (in module microglia_analyzer.tiles.tiler) microglia_analyzer module microglia_analyzer.custom_loss module microglia_analyzer.ma_worker module microglia_analyzer.qt_workers module microglia_analyzer.tiles module microglia_analyzer.tiles.patch module microglia_analyzer.tiles.plot module microglia_analyzer.tiles.recalibrate module microglia_analyzer.tiles.tiler module

microglia_analyzer.unet_worker module microglia_analyzer.utils module MicrogliaAnalyzer (class in microglia_analyzer.ma_worker) module microglia_analyzer microglia_analyzer.custom_loss microglia_analyzer.ma_worker microglia_analyzer.qt_workers microglia_analyzer.tiles microglia_analyzer.tiles.patch microglia_analyzer.tiles.plot microglia_analyzer.tiles.recalibrate microglia_analyzer.tiles.tiler microglia_analyzer.unet_worker microglia_analyzer.utils

N

normalize() (in module microglia_analyzer.tiles.tiler)

normalize_batch() (in module microglia_analyzer.utils)

P

Patch2D (class in microglia_analyzer.tiles.patch)

plot_patches_layout() (in module microglia_analyzer.tiles.plot) process_factor() (in module microglia_analyzer.tiles.recalibrate)

Q

QtBatchRunners (class in microglia_analyzer.qt_workers) QtClassifyMicroglia (class in microglia_analyzer.qt_workers)

QtMeasureMicroglia (class in microglia_analyzer.qt_workers) QtSegmentMicroglia (class in microglia_analyzer.qt_workers)

R

recalibrate_image() (in module microglia_analyzer.tiles.recalibrate) recalibrate_shape() (in module microglia_analyzer.tiles.recalibrate) reset_classification() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method) reset_segmentation() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method)

run() (microglia_analyzer.qt_workers.QtBatchRunners method) (microglia_analyzer.qt_workers.QtClassifyMicroglia method) (microglia_analyzer.qt_workers.QtMeasureMicroglia method) (microglia_analyzer.qt_workers.QtSegmentMicroglia method)

S

save_as_fake_colors() (in module microglia_analyzer.utils) segment_microglia() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method) set_calibration() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method) set_classification_model() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method)

set_input_image() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method) set_min_surface() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method) set_proba_threshold() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method) set_segmentation_model() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method) set_working_directory() (microglia_analyzer.ma_worker.MicrogliaAnalyzer method)

T

TIFF_REGEX (in module microglia_analyzer)

tiles_to_image() (microglia_analyzer.tiles.tiler.ImageTiler2D method) to_kill (microglia_analyzer.qt_workers.QtBatchRunners attribute)

U

UNetWorker (class in microglia_analyzer.unet_worker) update (microglia_analyzer.qt_workers.QtBatchRunners attribute) (microglia_analyzer.qt_workers.QtClassifyMicroglia attribute) (microglia_analyzer.qt_workers.QtMeasureMicroglia attribute) (microglia_analyzer.qt_workers.QtSegmentMicroglia attribute)

W

workflow() (microglia_analyzer.qt_workers.QtBatchRunners method) write_classification() (microglia_analyzer.qt_workers.QtBatchRunners method) write_csv() (microglia_analyzer.qt_workers.QtBatchRunners method)

write_mask() (microglia_analyzer.qt_workers.QtBatchRunners method) write_skeleton() (microglia_analyzer.qt_workers.QtBatchRunners method) write_tsv() (microglia_analyzer.qt_workers.QtBatchRunners method) write_visual_check() (microglia_analyzer.qt_workers.QtBatchRunners method)