An advanced version of the omnipose detector.

With a gotcha: omnipose is based on cellpose 1, so there is no 'cellprob_threshld_ parameter, but 'mask_threshold' instead.
trackmate-sc · Nov 6, 2023 · 8b266ca · 8b266ca
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diff --git a/...a/fiji/plugin/trackmate/omnipose/advanced/AdvancedOmniposeDetectorConfigurationPanel.java b/...a/fiji/plugin/trackmate/omnipose/advanced/AdvancedOmniposeDetectorConfigurationPanel.java
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+package fiji.plugin.trackmate.omnipose.advanced;
+
+import static fiji.plugin.trackmate.cellpose.advanced.AdvancedCellposeDetectorFactory.KEY_CELL_PROB_THRESHOLD;
+import static fiji.plugin.trackmate.cellpose.advanced.AdvancedCellposeDetectorFactory.KEY_FLOW_THRESHOLD;
+import static fiji.plugin.trackmate.gui.Fonts.SMALL_FONT;
+
+import java.awt.GridBagConstraints;
+import java.awt.Insets;
+import java.util.Map;
+
+import javax.swing.JLabel;
+
+import fiji.plugin.trackmate.Model;
+import fiji.plugin.trackmate.Settings;
+import fiji.plugin.trackmate.cellpose.advanced.AdvancedCellposeDetectorConfigurationPanel;
+import fiji.plugin.trackmate.detection.SpotDetectorFactoryBase;
+import fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble;
+import fiji.plugin.trackmate.gui.displaysettings.StyleElements;
+import fiji.plugin.trackmate.omnipose.OmniposeDetectorConfigurationPanel;
+import fiji.plugin.trackmate.omnipose.OmniposeSettings.PretrainedModelOmnipose;
+
+public class AdvancedOmniposeDetectorConfigurationPanel extends OmniposeDetectorConfigurationPanel
+{
+
+	private static final long serialVersionUID = 1L;
+
+	private static final String TITLE = AdvancedOmniposeDetectorFactory.NAME;;
+
+	private final StyleElements.BoundedDoubleElement flowThresholdEl = new StyleElements.BoundedDoubleElement( "Flow threshold", 0.0, 3.0 )
+	{
+
+		private double flowThreshold = 0.;
+
+		@Override
+		public double get()
+		{
+			return flowThreshold;
+		}
+
+		@Override
+		public void set( final double v )
+		{
+			flowThreshold = v;
+		}
+	};
+
+	private final StyleElements.BoundedDoubleElement cellProbThresholdEl = new StyleElements.BoundedDoubleElement("Cell prob", -6.0, 6.0)
+	{
+
+		private double cellProbThreshold = 0.;
+
+		@Override
+		public double get()
+		{
+			return cellProbThreshold;
+		}
+
+		@Override
+		public void set( final double v )
+		{
+			cellProbThreshold = v;
+		}
+	};
+
+	public AdvancedOmniposeDetectorConfigurationPanel( final Settings settings, final Model model )
+	{
+		super( settings, model, TITLE, ICON, DOC1_URL, "omnipose", PretrainedModelOmnipose.values() );
+
+		/*
+		 * Add flow threshold.
+		 */
+
+		int gridy = 12;
+
+		final JLabel lblFlowThreshold = new JLabel( "Flow threshold:" );
+		lblFlowThreshold.setFont( SMALL_FONT );
+		final GridBagConstraints gbcLblFlowThreshold = new GridBagConstraints();
+		gbcLblFlowThreshold.anchor = GridBagConstraints.EAST;
+		gbcLblFlowThreshold.insets = new Insets( 0, 5, 5, 5 );
+		gbcLblFlowThreshold.gridx = 0;
+		gbcLblFlowThreshold.gridy = gridy;
+		add( lblFlowThreshold, gbcLblFlowThreshold );
+
+		final SliderPanelDouble sliderPanelFlowThreshold = StyleElements.linkedSliderPanel( flowThresholdEl, 3, 0.1 );
+		AdvancedCellposeDetectorConfigurationPanel.setFont( sliderPanelFlowThreshold, SMALL_FONT );
+		final GridBagConstraints gbcFlowThresholdSlider = new GridBagConstraints();
+		gbcFlowThresholdSlider.anchor = GridBagConstraints.EAST;
+		gbcFlowThresholdSlider.insets = new Insets( 0, 5, 5, 5 );
+		gbcFlowThresholdSlider.fill = GridBagConstraints.HORIZONTAL;
+		gbcFlowThresholdSlider.gridx = 1;
+		gbcFlowThresholdSlider.gridwidth = 2;
+		gbcFlowThresholdSlider.gridy = gridy;
+		add( sliderPanelFlowThreshold, gbcFlowThresholdSlider );
+
+		/*
+		 * Add cell probability threshold.
+		 */
+
+		gridy++;
+
+		final JLabel lblCellProb = new JLabel( "Mask threshold:" );
+		lblCellProb.setFont( SMALL_FONT );
+		final GridBagConstraints gbcLblCellProb = new GridBagConstraints();
+		gbcLblCellProb.anchor = GridBagConstraints.EAST;
+		gbcLblCellProb.insets = new Insets( 0, 5, 5, 5 );
+		gbcLblCellProb.gridx = 0;
+		gbcLblCellProb.gridy = gridy;
+		add( lblCellProb, gbcLblCellProb );
+
+		final SliderPanelDouble sliderPanelCellProbThreshold = StyleElements.linkedSliderPanel( cellProbThresholdEl, 3, 0.4 );
+		AdvancedCellposeDetectorConfigurationPanel.setFont( sliderPanelCellProbThreshold, SMALL_FONT );
+		final GridBagConstraints gbcCellProbThresholdSlider = new GridBagConstraints();
+		gbcCellProbThresholdSlider.anchor = GridBagConstraints.EAST;
+		gbcCellProbThresholdSlider.insets = new Insets( 0, 5, 5, 5 );
+		gbcCellProbThresholdSlider.fill = GridBagConstraints.HORIZONTAL;
+		gbcCellProbThresholdSlider.gridx = 1;
+		gbcCellProbThresholdSlider.gridwidth = 2;
+		gbcCellProbThresholdSlider.gridy = gridy;
+		add( sliderPanelCellProbThreshold, gbcCellProbThresholdSlider );
+	}
+
+	@Override
+	protected SpotDetectorFactoryBase< ? > getDetectorFactory()
+	{
+		return new AdvancedOmniposeDetectorFactory<>();
+	}
+
+	@Override
+	public void setSettings( final Map< String, Object > settings )
+	{
+		super.setSettings( settings );
+		flowThresholdEl.set( ( double ) settings.get( KEY_FLOW_THRESHOLD ) );
+		flowThresholdEl.update();
+		cellProbThresholdEl.set( ( double ) settings.get( KEY_CELL_PROB_THRESHOLD ) );
+		cellProbThresholdEl.update();
+	}
+
+	@Override
+	public Map< String, Object > getSettings()
+	{
+		final Map< String, Object > settings = super.getSettings();
+		settings.put( KEY_FLOW_THRESHOLD, flowThresholdEl.get() );
+		settings.put( KEY_CELL_PROB_THRESHOLD, cellProbThresholdEl.get() );
+		return settings;
+	}
+}