.. _modules: Empanada-napari modules ----------------------- .. _new-features: ======================== New and updated modules ======================== .. grid:: 3 :gutter: 4 4 5 5 :padding: 2 2 0 0 .. grid-item-card:: Export Segmentations :shadow: md Exports 2D stack segmentations or a single 3D volume label mask. +++ .. button-ref:: export-seg :ref-type: ref :click-parent: :color: primary :expand: Export Segmentations .. grid-item-card:: Morph Labels :shadow: md Applies morphological operations to specific labels or to the entire label layer. +++ .. button-ref:: morph-labels :ref-type: ref :click-parent: :color: primary :expand: Morph Labels .. grid-item-card:: Count Labels :shadow: md Counts the number of label IDs in the dataset and export the list of label IDs in an Excel workbook. +++ .. button-ref:: count-labels :ref-type: ref :click-parent: :color: primary :expand: Count Labels .. grid-item-card:: Filter Labels :shadow: md Removes small pixel/voxel valued labels from the label mask and/or labels touching the border of the image. +++ .. button-ref:: filter-labels :ref-type: ref :click-parent: :color: primary :expand: Filter Labels .. grid-item-card:: Split Labels :shadow: md Allows the placement of multiple markers for distance watershed-based instance splitting. +++ .. button-ref:: split-labels :ref-type: ref :click-parent: :color: primary :expand: Split Labels .. grid-item-card:: Export a model :shadow: md Locally exports an empanada model. Useful for sharing models locally or over the internet. +++ .. button-ref:: export-model :ref-type: ref :click-parent: :color: primary :expand: Export a Model .. grid-item-card:: Import a model :shadow: md Makes a new model accessible in all other training and inference modules. +++ .. button-ref:: import-model :ref-type: ref :click-parent: :color: primary :expand: Import a Model .. _inference-modules: ================================= Inference modules ================================= .. grid:: 2 :gutter: 3 3 4 5 :padding: 2 2 0 0 .. grid-item-card:: 2D Inference (Parameter testing) :shadow: md Runs model inference on 2D images. Supports batch mode for predicting segmentations on a series of unrelated images or can be used to segment arbitrary 2D slices from volumetric data. +++ .. button-ref:: 2d-inference :ref-type: ref :click-parent: :color: primary :expand: 2D Inference (Parameter Testing) .. grid-item-card:: 3D Inference :shadow: md Implements stack and ortho-plane inference functionality for volumetric datasets. +++ .. button-ref:: 3d-inference :ref-type: ref :click-parent: :color: primary :expand: 3D Inference .. _finetune-train-mods: ================================= Finetune and training modules ================================= .. grid:: 3 :gutter: 3 3 4 5 :padding: 2 2 0 0 .. grid-item-card:: Pick finetune/training patches :shadow: md Automatically picks patches of data to annotate from 2D or 3D images. Also gives the option for uses for manually select ROIs using placed points. +++ .. button-ref:: pick-patches :ref-type: ref :click-parent: :color: primary :expand: Pick Patches .. grid-item-card:: Save finetune/training patches :shadow: md Stores training patch segmentations in the correct format expected for model finetuning and training. +++ .. button-ref:: save-patches :ref-type: ref :click-parent: :color: primary :expand: Save Patches .. grid-item-card:: Finetune a model :shadow: md Allows users to finetune any registered model on a specialized segmentation dataset. +++ .. button-ref:: finetune-model :ref-type: ref :click-parent: :color: primary :expand: Finetune a Model .. grid-item-card:: Train a model :shadow: md Train models from scratch for arbitrary panoptic segmentation tasks. Optionally, initialize training from CEM pre-trained weights for faster convergence and greater robustness. +++ .. button-ref:: train-model :ref-type: ref :click-parent: :color: primary :expand: Train a Model .. grid-item-card:: Register a model :shadow: md Make a new model accessible in all other training and inference modules. Models can be registered from .pth files or from web URLs. Useful for sharing models locally or over the internet. +++ .. button-ref:: register-model :ref-type: ref :click-parent: :color: primary :expand: Register a Model .. grid-item-card:: Get model info :shadow: md Get information about registered models to help decide which one is appropriate for inference or finetuning. +++ .. button-ref:: get-model-info :ref-type: ref :click-parent: :color: primary :expand: Get Model Info .. _proofreading-tools: ================================= Proofreading modules ================================= .. grid:: 4 :gutter: 2 2 4 4 :padding: 2 2 0 0 .. grid-item-card:: Merge Labels :shadow: md Allows the selection of multiple instances and merges them all to the same label. +++ .. button-ref:: merge-labels :ref-type: ref :click-parent: :color: primary :expand: Merge Labels .. grid-item-card:: Delete Labels :shadow: md Allows the selection of multiple instances and allows the removal of selected labels +++ .. button-ref:: delete-labels :ref-type: ref :click-parent: :color: primary :expand: Delete Labels .. grid-item-card:: Jump to label :shadow: md Given a label ID, moves the napari viewer to the first 2D slice where an object appears. +++ .. button-ref:: jump :ref-type: ref :click-parent: :color: primary :expand: Jump to Label .. grid-item-card:: Find next available label :shadow: md Returns the next available label ID for manual annotation. +++ .. button-ref:: find-next :ref-type: ref :click-parent: :color: primary :expand: Find Next Label .. toctree:: :caption: Inference :hidden: 2D Inference (Parameter Testing) <../modules/_2d_seg> 3D Inference <../modules/_3d_seg> Export Segmentations <../modules/_export_segmentation> .. toctree:: :caption: Finetuning and Training a Model :hidden: Pick finetune/training patches <../modules/_pick_patches> Save finetune/training patches <../modules/_save_patches> Finetune a model <../modules/_finetune> Train a model <../modules/_train> Register a model <../modules/_register_model> Get model info <../modules/_get_info> Export a model <../modules/_export> Import a model <../modules/_import> .. toctree:: :caption: Proofreading Tools :hidden: Count Labels <../modules/_count> Merge Labels <../modules/_merge> Delete Labels <../modules/_delete> Morph Labels <../modules/_morph> Split Labels <../modules/_split> Filter Labels <../modules/_filter> Jump to Label <../modules/_jump> Find Next Available Label <../modules/_find_next>