├── .gitignore ├── LICENSE ├── README.md ├── cell_tracker ├── __init__.py ├── __main__ .py ├── interface │ ├── __init__.py │ ├── components │ │ ├── __init__.py │ │ ├── correction_tools.py │ │ ├── file_tree.py │ │ ├── frame.py │ │ ├── left_navigation.py │ │ ├── left_tools.py │ │ ├── left_tools_annotation.py │ │ ├── left_tools_data_loader.py │ │ ├── left_tools_io.py │ │ ├── left_tools_loss.py │ │ ├── left_tools_normalization.py │ │ ├── left_tools_optimizer.py │ │ ├── left_tools_output.py │ │ ├── left_tools_run_train.py │ │ ├── left_tools_segment.py │ │ ├── left_tools_track.py │ │ ├── left_tools_trainer.py │ │ ├── left_tools_weighted_loss.py │ │ ├── menu.py │ │ ├── message_box.py │ │ ├── popup_window.py │ │ ├── status_bar.py │ │ └── visualize.py │ ├── config.py │ ├── icon │ │ ├── Arrow_down.png │ │ ├── Arrow_right.png │ │ ├── algorithm.png │ │ ├── annotation.png │ │ ├── browse.png │ │ ├── cell.png │ │ ├── check.png │ │ ├── circle.png │ │ ├── close.png │ │ ├── delete.png │ │ ├── eraser.png │ │ ├── eraser1.png │ │ ├── hand.png │ │ ├── hand1.png │ │ ├── info.png │ │ ├── left.png │ │ ├── left1.png │ │ ├── network_train.png │ │ ├── open.png │ │ ├── pen.png │ │ ├── pen1.png │ │ ├── pre_progress.png │ │ ├── project_management.png │ │ ├── question.png │ │ ├── right.png │ │ ├── right1.png │ │ ├── square-plus.png │ │ ├── switch.png │ │ ├── trash.png │ │ └── warning.png │ ├── main_interface.py │ └── utils │ │ ├── __init__.py │ │ ├── color.py │ │ ├── files.py │ │ ├── frontend_property.py │ │ └── img_process.py ├── normalizers │ ├── __init__.py │ ├── equalize_hist.py │ ├── min_max.py │ └── retinex.py ├── segmenters │ ├── __init__.py │ ├── customized │ │ ├── __init__.py │ │ └── customized.py │ ├── tradition_methods │ │ ├── grabcut.py │ │ ├── threshold.py │ │ └── watershed.py │ ├── unet │ │ ├── __init__.py │ │ ├── backbone │ │ │ ├── __init__.py │ │ │ └── unet.py │ │ ├── configs │ │ │ ├── __init__.py │ │ │ └── config.py │ │ ├── dataset │ │ │ ├── __init__.py │ │ │ ├── augmentation.py │ │ │ ├── benchmark.py │ │ │ ├── cell.py │ │ │ ├── dataloader.py │ │ │ ├── utils.py │ │ │ └── weighted_label.py │ │ ├── loss │ │ │ ├── __init__.py │ │ │ └── loss.py │ │ ├── train.py │ │ ├── trainer │ │ │ ├── __init__.py │ │ │ └── trainer.py │ │ ├── unet.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── logger.py │ │ │ ├── meters.py │ │ │ ├── post_process.py │ │ │ └── utils.py │ └── utils │ │ ├── __init__.py │ │ └── processing.py ├── trackers │ ├── __init__.py │ ├── bipartite │ │ ├── __init__.py │ │ ├── bipartite_tracker.py │ │ └── tracks.py │ ├── components │ │ ├── __init__.py │ │ ├── kalman_filter.py │ │ └── recorder.py │ └── utils │ │ ├── __init__.py │ │ ├── bbox.py │ │ ├── configs.py │ │ └── infer.py ├── utils │ ├── __init__.py │ ├── logger.py │ └── utils.py └── writer │ ├── __init__.py │ ├── templates │ └── results.html │ ├── utils.py │ ├── visualize.py │ └── writer.py ├── datasets ├── demo-dataset1 │ ├── 000000.jpg │ ├── 000001.jpg │ ├── 000002.jpg │ ├── 000003.jpg │ ├── 000004.jpg │ ├── 000005.jpg │ ├── 000006.jpg │ ├── 000007.jpg │ ├── 000008.jpg │ ├── 000009.jpg │ ├── 000010.jpg │ ├── 000011.jpg │ ├── 000012.jpg │ ├── 000013.jpg │ ├── 000014.jpg │ ├── 000015.jpg │ ├── 000016.jpg │ ├── 000017.jpg │ ├── 000018.jpg │ ├── 000019.jpg │ ├── 000020.jpg │ ├── 000021.jpg │ ├── 000022.jpg │ ├── 000023.jpg │ ├── 000024.jpg │ ├── 000025.jpg │ ├── 000026.jpg │ ├── 000027.jpg │ ├── 000028.jpg │ ├── 000029.jpg │ ├── 000030.jpg │ ├── 000031.jpg │ ├── 000032.jpg │ ├── 000033.jpg │ ├── 000034.jpg │ ├── 000035.jpg │ ├── 000036.jpg │ ├── 000037.jpg │ ├── 000038.jpg │ ├── 000039.jpg │ ├── 000040.jpg │ ├── 000041.jpg │ ├── 000042.jpg │ ├── 000043.jpg │ ├── 000044.jpg │ ├── 000045.jpg │ ├── 000046.jpg │ ├── 000047.jpg │ ├── 000048.jpg │ ├── 000049.jpg │ ├── 000050.jpg │ ├── 000051.jpg │ ├── 000052.jpg │ ├── 000053.jpg │ ├── 000054.jpg │ ├── 000055.jpg │ ├── 000056.jpg │ ├── 000057.jpg │ ├── 000058.jpg │ ├── 000059.jpg │ ├── 000060.jpg │ ├── 000061.jpg │ ├── 000062.jpg │ ├── 000063.jpg │ └── 000064.jpg └── demo-dataset2 │ ├── 000000.jpg │ ├── 000001.jpg │ ├── 000002.jpg │ ├── 000003.jpg │ ├── 000004.jpg │ ├── 000005.jpg │ ├── 000006.jpg │ ├── 000007.jpg │ ├── 000008.jpg │ ├── 000009.jpg │ ├── 000010.jpg │ ├── 000011.jpg │ ├── 000012.jpg │ ├── 000013.jpg │ ├── 000014.jpg │ ├── 000015.jpg │ ├── 000016.jpg │ ├── 000017.jpg │ ├── 000018.jpg │ ├── 000019.jpg │ ├── 000020.jpg │ ├── 000021.jpg │ ├── 000022.jpg │ ├── 000023.jpg │ ├── 000024.jpg │ ├── 000025.jpg │ ├── 000026.jpg │ ├── 000027.jpg │ ├── 000028.jpg │ ├── 000029.jpg │ ├── 000030.jpg │ ├── 000031.jpg │ ├── 000032.jpg │ ├── 000033.jpg │ ├── 000034.jpg │ ├── 000035.jpg │ ├── 000036.jpg │ ├── 000037.jpg │ ├── 000038.jpg │ ├── 000039.jpg │ ├── 000040.jpg │ ├── 000041.jpg │ ├── 000042.jpg │ ├── 000043.jpg │ ├── 000044.jpg │ ├── 000045.jpg │ ├── 000046.jpg │ ├── 000047.jpg │ ├── 000048.jpg │ ├── 000049.jpg │ ├── 000050.jpg │ ├── 000051.jpg │ ├── 000052.jpg │ ├── 000053.jpg │ ├── 000054.jpg │ ├── 000055.jpg │ ├── 000056.jpg │ ├── 000057.jpg │ ├── 000058.jpg │ ├── 000059.jpg │ ├── 000060.jpg │ ├── 000061.jpg │ ├── 000062.jpg │ ├── 000063.jpg │ ├── 000064.jpg │ ├── 000065.jpg │ ├── 000066.jpg │ ├── 000067.jpg │ ├── 000068.jpg │ ├── 000069.jpg │ ├── 000070.jpg │ ├── 000071.jpg │ ├── 000072.jpg │ ├── 000073.jpg │ ├── 000074.jpg │ ├── 000075.jpg │ ├── 000076.jpg │ ├── 000077.jpg │ ├── 000078.jpg │ ├── 000079.jpg │ ├── 000080.jpg │ ├── 000081.jpg │ ├── 000082.jpg │ ├── 000083.jpg │ ├── 000084.jpg │ ├── 000085.jpg │ ├── 000086.jpg │ ├── 000087.jpg │ ├── 000088.jpg │ ├── 000089.jpg │ ├── 000090.jpg │ ├── 000091.jpg │ ├── 000092.jpg │ ├── 000093.jpg │ ├── 000094.jpg │ ├── 000095.jpg │ ├── 000096.jpg │ ├── 000097.jpg │ ├── 000098.jpg │ ├── 000099.jpg │ ├── 000100.jpg │ ├── 000101.jpg │ ├── 000102.jpg │ ├── 000103.jpg │ ├── 000104.jpg │ ├── 000105.jpg │ ├── 000106.jpg │ ├── 000107.jpg │ ├── 000108.jpg │ ├── 000109.jpg │ ├── 000110.jpg │ ├── 000111.jpg │ ├── 000112.jpg │ ├── 000113.jpg │ ├── 000114.jpg │ ├── 000115.jpg │ ├── 000116.jpg │ ├── 000117.jpg │ ├── 000118.jpg │ ├── 000119.jpg │ ├── 000120.jpg │ ├── 000121.jpg │ ├── 000122.jpg │ ├── 000123.jpg │ ├── 000124.jpg │ ├── 000125.jpg │ ├── 000126.jpg │ └── 000127.jpg ├── doc └── CellTrackerTutorial.pdf ├── imgs └── interface.png ├── main.py ├── requirements.txt ├── training_demo1 ├── label_img │ ├── man_seg000.tif │ ├── man_seg001.tif │ ├── man_seg002.tif │ ├── man_seg003.tif │ ├── man_seg004.tif │ ├── man_seg005.tif │ ├── man_seg006.tif │ ├── man_seg007.tif │ ├── man_seg008.tif │ ├── man_seg009.tif │ ├── man_seg010.tif │ ├── man_seg011.tif │ ├── man_seg012.tif │ ├── man_seg013.tif │ ├── man_seg014.tif │ ├── man_seg015.tif │ ├── man_seg016.tif │ ├── man_seg017.tif │ ├── man_seg018.tif │ ├── man_seg019.tif │ ├── man_seg020.tif │ ├── man_seg021.tif │ ├── man_seg022.tif │ ├── man_seg023.tif │ ├── man_seg024.tif │ ├── man_seg025.tif │ ├── man_seg026.tif │ ├── man_seg027.tif │ ├── man_seg028.tif │ ├── man_seg029.tif │ ├── man_seg030.tif │ ├── man_seg031.tif │ ├── man_seg032.tif │ ├── man_seg033.tif │ ├── man_seg034.tif │ ├── man_seg035.tif │ ├── man_seg036.tif │ ├── man_seg037.tif │ ├── man_seg038.tif │ ├── man_seg039.tif │ ├── man_seg040.tif │ ├── man_seg041.tif │ ├── man_seg042.tif │ ├── man_seg043.tif │ ├── man_seg044.tif │ ├── man_seg045.tif │ ├── man_seg046.tif │ ├── man_seg047.tif │ ├── man_seg048.tif │ ├── man_seg049.tif │ ├── man_seg050.tif │ ├── man_seg051.tif │ ├── man_seg052.tif │ ├── man_seg053.tif │ ├── man_seg054.tif │ ├── man_seg055.tif │ ├── man_seg056.tif │ ├── man_seg057.tif │ ├── man_seg058.tif │ ├── man_seg059.tif │ ├── man_seg060.tif │ ├── man_seg061.tif │ ├── man_seg062.tif │ ├── man_seg063.tif │ └── man_seg064.tif ├── retraining.py └── source_img │ ├── t000.tif │ ├── t001.tif │ ├── t002.tif │ ├── t003.tif │ ├── t004.tif │ ├── t005.tif │ ├── t006.tif │ ├── t007.tif │ ├── t008.tif │ ├── t009.tif │ ├── t010.tif │ ├── t011.tif │ ├── t012.tif │ ├── t013.tif │ ├── t014.tif │ ├── t015.tif │ ├── t016.tif │ ├── t017.tif │ ├── t018.tif │ ├── t019.tif │ ├── t020.tif │ ├── t021.tif │ ├── t022.tif │ ├── t023.tif │ ├── t024.tif │ ├── t025.tif │ ├── t026.tif │ ├── t027.tif │ ├── t028.tif │ ├── t029.tif │ ├── t030.tif │ ├── t031.tif │ ├── t032.tif │ ├── t033.tif │ ├── t034.tif │ ├── t035.tif │ ├── t036.tif │ ├── t037.tif │ ├── t038.tif │ ├── t039.tif │ ├── t040.tif │ ├── t041.tif │ ├── t042.tif │ ├── t043.tif │ ├── t044.tif │ ├── t045.tif │ ├── t046.tif │ ├── t047.tif │ ├── t048.tif │ ├── t049.tif │ ├── t050.tif │ ├── t051.tif │ ├── t052.tif │ ├── t053.tif │ ├── t054.tif │ ├── t055.tif │ ├── t056.tif │ ├── t057.tif │ ├── t058.tif │ ├── t059.tif │ ├── t060.tif │ ├── t061.tif │ ├── t062.tif │ ├── t063.tif │ └── t064.tif └── training_demo2 ├── label_img ├── annotation_000000.png ├── annotation_000001.png ├── annotation_000002.png ├── annotation_000003.png └── annotation_000004.png ├── retraining.py └── source_img ├── 000000.jpg ├── 000001.jpg ├── 000002.jpg ├── 000003.jpg └── 000004.jpg 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