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locpix 0.1.0.1.dev8+g1a8e0b3.d20240209 documentation - Home
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  • locpix.evaluate
    • locpix.evaluate.metrics
      • locpix.evaluate.metrics.aggregated_metrics
      • locpix.evaluate.metrics.mean_metrics
      • locpix.evaluate.metrics.metric_calculation
  • locpix.img_processing
    • locpix.img_processing.data_loading
      • locpix.img_processing.data_loading.dataset
        • locpix.img_processing.data_loading.dataset.ImgDataset
      • locpix.img_processing.data_loading.transforms
        • locpix.img_processing.data_loading.transforms.transform
    • locpix.img_processing.models
      • locpix.img_processing.models.unet
        • locpix.img_processing.models.unet.DoubleConv
        • locpix.img_processing.models.unet.Down
        • locpix.img_processing.models.unet.OutConv
        • locpix.img_processing.models.unet.Up
        • locpix.img_processing.models.unet.two_d_UNet
    • locpix.img_processing.render
      • locpix.img_processing.render.visualise_seg_item
    • locpix.img_processing.training
      • locpix.img_processing.training.loss
        • locpix.img_processing.training.loss.dice_loss
      • locpix.img_processing.training.train
        • locpix.img_processing.training.train.train_loop
    • locpix.img_processing.watershed
      • locpix.img_processing.watershed.get_markers
      • locpix.img_processing.watershed.watershed_segment
      • locpix.img_processing.watershed.WatershedWidget
  • locpix.preprocessing
    • locpix.preprocessing.datastruc
      • locpix.preprocessing.datastruc.item
    • locpix.preprocessing.functions
      • locpix.preprocessing.functions.file_to_datastruc
  • locpix.scripts
    • locpix.scripts.development
      • locpix.scripts.development.clean_up
      • locpix.scripts.development.file_names
        • locpix.scripts.development.file_names.main
      • locpix.scripts.development.licenses
        • locpix.scripts.development.licenses.get_pkg_license
        • locpix.scripts.development.licenses.print_packages_and_licenses
    • locpix.scripts.img_seg
      • locpix.scripts.img_seg.agg_metrics
        • locpix.scripts.img_seg.agg_metrics.main
      • locpix.scripts.img_seg.cellpose_eval
        • locpix.scripts.img_seg.cellpose_eval.main
      • locpix.scripts.img_seg.cellpose_train
        • locpix.scripts.img_seg.cellpose_train.main
      • locpix.scripts.img_seg.classic
        • locpix.scripts.img_seg.classic.main
      • locpix.scripts.img_seg.ilastik_output
        • locpix.scripts.img_seg.ilastik_output.main
      • locpix.scripts.img_seg.ilastik_prep
        • locpix.scripts.img_seg.ilastik_prep.main
      • locpix.scripts.img_seg.img_train_prep
        • locpix.scripts.img_seg.img_train_prep.clean_up
        • locpix.scripts.img_seg.img_train_prep.clean_up_all
        • locpix.scripts.img_seg.img_train_prep.parquet_2_img
        • locpix.scripts.img_seg.img_train_prep.preprocess_all_files
        • locpix.scripts.img_seg.img_train_prep.preprocess_train_files
      • locpix.scripts.img_seg.membrane_performance
        • locpix.scripts.img_seg.membrane_performance.main
      • locpix.scripts.img_seg.membrane_performance_method
        • locpix.scripts.img_seg.membrane_performance_method.main
      • locpix.scripts.img_seg.train_prep
        • locpix.scripts.img_seg.train_prep.main
      • locpix.scripts.img_seg.unet_train
        • locpix.scripts.img_seg.unet_train.main
    • locpix.scripts.preprocessing
      • locpix.scripts.preprocessing.annotate
        • locpix.scripts.preprocessing.annotate.main
      • locpix.scripts.preprocessing.preprocess
        • locpix.scripts.preprocessing.preprocess.main
        • locpix.scripts.preprocessing.preprocess.project_info
  • locpix.templates
  • locpix.visualise
    • locpix.visualise.performance
      • locpix.visualise.performance.generate_binary_conf_matrix
      • locpix.visualise.performance.plot_pr_curve
    • locpix.visualise.vis_img
      • locpix.visualise.vis_img.img_2_grey
      • locpix.visualise.vis_img.label_2_4_colours
      • locpix.visualise.vis_img.manual_threshold
      • locpix.visualise.vis_img.plot_img
      • locpix.visualise.vis_img.visualise_seg
  • locpix
  • locpix.scripts
  • locpix.scrip...

locpix.scripts.preprocessing#

Modules

locpix.scripts.preprocessing.annotate

Annotate module

locpix.scripts.preprocessing.preprocess

Preprocessing module

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locpix.scripts.img_seg.unet_train.main

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