Examples with ImageData qupath.lib.images.ImageData used on opensource projects

Example 1 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class ProjectImportImagesCommand method getThumbnailRGB.

// /**
// * Add a single ImageServer to a project, without considering sub-images.
// * <p>
// * This includes an optional attempt to request a thumbnail; if this fails, the image will not be added.
// *
// * @param project the project to which the entry should be added
// * @param server the server to add
// * @param type the ImageType that should be set for each entry being added
// * @return
// */
// public static ProjectImageEntry<BufferedImage> addSingleImageToProject(Project<BufferedImage> project, ImageServer<BufferedImage> server, ImageType type) {
// ProjectImageEntry<BufferedImage> entry = null;
// try {
// var img = getThumbnailRGB(server, null);
// entry = project.addImage(server);
// if (entry != null) {
// // Write a thumbnail if we can
// entry.setThumbnail(img);
// // Initialize an ImageData object with a type, if required
// if (type != null) {
// var imageData = new ImageData<>(server, type);
// entry.saveImageData(imageData);
// }
// }
// } catch (IOException e) {
// logger.warn("Error attempting to add " + server, e);
// }
// return entry;
// }
public static BufferedImage getThumbnailRGB(ImageServer<BufferedImage> server, ImageDisplay imageDisplay) throws IOException {
    var img2 = server.getDefaultThumbnail(server.nZSlices() / 2, 0);
    // Try to write RGB images directly
    boolean success = false;
    if (imageDisplay == null && (server.isRGB() || img2.getType() == BufferedImage.TYPE_BYTE_GRAY)) {
        return resizeForThumbnail(img2);
    }
    if (!success) {
        // Try with display transforms
        if (imageDisplay == null) {
            // By wrapping the thumbnail, we avoid slow z-stack/time series requests & determine brightness & contrast just from one plane
            var wrappedServer = new WrappedBufferedImageServer("Dummy", img2, server.getMetadata().getChannels());
            imageDisplay = new ImageDisplay(new ImageData<>(wrappedServer));
        // imageDisplay = new ImageDisplay(new ImageData<>(server));
        }
        for (ChannelDisplayInfo info : imageDisplay.selectedChannels()) {
            imageDisplay.autoSetDisplayRange(info);
        }
        img2 = imageDisplay.applyTransforms(img2, null);
        return resizeForThumbnail(img2);
    }
    return img2;
}

Example 2 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class Commands method requestShapeFeatures.

private static void requestShapeFeatures(ImageData<?> imageData, Collection<ShapeFeatures> features) {
    if (imageData == null)
        return;
    var featureArray = features.toArray(ShapeFeatures[]::new);
    if (featureArray.length == 0)
        return;
    Collection<PathObject> selected = imageData.getHierarchy().getSelectionModel().getSelectedObjects();
    if (selected.isEmpty()) {
        Dialogs.showWarningNotification("Shape features", "No objects selected!");
    } else {
        selected = new ArrayList<>(selected);
        String featureString = Arrays.stream(featureArray).map(f -> "\"" + f.name() + "\"").collect(Collectors.joining(", "));
        QP.addShapeMeasurements(imageData, selected, featureArray);
        imageData.getHistoryWorkflow().addStep(new DefaultScriptableWorkflowStep("Add shape measurements", String.format("addShapeMeasurements(%s)", featureString)));
        if (selected.size() == 1)
            Dialogs.showInfoNotification("Shape features", "Shape features calculated for one object");
        else
            Dialogs.showInfoNotification("Shape features", "Shape features calculated for " + selected.size() + " objects");
    }
}

Example 3 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class TMACommands method promptToExportTMAData.

/**
 * Prompt to export summary TMA data for a specific image to a directory.
 * @param qupath
 * @param imageData
 */
public static void promptToExportTMAData(QuPathGUI qupath, ImageData<BufferedImage> imageData) {
    String title = "Export TMA data";
    if (imageData == null) {
        Dialogs.showNoImageError(title);
        return;
    }
    PathObjectHierarchy hierarchy = imageData == null ? null : imageData.getHierarchy();
    if (hierarchy == null || hierarchy.isEmpty() || hierarchy.getTMAGrid() == null || hierarchy.getTMAGrid().nCores() == 0) {
        Dialogs.showErrorMessage(title, "No TMA data available!");
        return;
    }
    var overlayOptions = qupath.getViewers().stream().filter(v -> v.getImageData() == imageData).map(v -> v.getOverlayOptions()).findFirst().orElse(qupath.getOverlayOptions());
    String defaultName = ServerTools.getDisplayableImageName(imageData.getServer());
    File file = Dialogs.promptToSaveFile(null, null, defaultName, "TMA data", ".qptma");
    if (file != null) {
        if (!file.getName().endsWith(".qptma"))
            file = new File(file.getParentFile(), file.getName() + ".qptma");
        double downsample = PathPrefs.tmaExportDownsampleProperty().get();
        TMADataIO.writeTMAData(file, imageData, overlayOptions, downsample);
        WorkflowStep step = new DefaultScriptableWorkflowStep("Export TMA data", "exportTMAData(\"" + GeneralTools.escapeFilePath(file.getParentFile().getAbsolutePath()) + "\", " + downsample + ")");
        imageData.getHistoryWorkflow().addStep(step);
    // PathAwtIO.writeTMAData(file, imageData, viewer.getOverlayOptions(), Double.NaN);
    }
}

Example 4 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class QuPathGUI method setViewerPopupMenu.

private void setViewerPopupMenu(final QuPathViewerPlus viewer) {
    final ContextMenu popup = new ContextMenu();
    MenuItem miAddRow = new MenuItem("Add row");
    miAddRow.setOnAction(e -> viewerManager.addRow(viewer));
    MenuItem miAddColumn = new MenuItem("Add column");
    miAddColumn.setOnAction(e -> viewerManager.addColumn(viewer));
    MenuItem miRemoveRow = new MenuItem("Remove row");
    miRemoveRow.setOnAction(e -> viewerManager.removeViewerRow(viewer));
    MenuItem miRemoveColumn = new MenuItem("Remove column");
    miRemoveColumn.setOnAction(e -> viewerManager.removeViewerColumn(viewer));
    MenuItem miCloseViewer = new MenuItem("Close viewer");
    miCloseViewer.setOnAction(e -> {
        viewerManager.closeViewer(viewer);
    // viewerManager.removeViewer(viewer);
    });
    MenuItem miResizeGrid = new MenuItem("Reset grid size");
    miResizeGrid.setOnAction(e -> {
        viewerManager.resetGridSize();
    });
    MenuItem miToggleSync = ActionTools.createCheckMenuItem(defaultActions.TOGGLE_SYNCHRONIZE_VIEWERS, null);
    MenuItem miMatchResolutions = ActionTools.createMenuItem(defaultActions.MATCH_VIEWER_RESOLUTIONS);
    Menu menuMultiview = MenuTools.createMenu("Multi-view", miToggleSync, miMatchResolutions, miCloseViewer, null, miResizeGrid, null, // null,
    miAddRow, miAddColumn, null, miRemoveRow, miRemoveColumn);
    Menu menuView = MenuTools.createMenu("Display", ActionTools.createCheckMenuItem(defaultActions.SHOW_ANALYSIS_PANE, null), defaultActions.BRIGHTNESS_CONTRAST, null, ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 0.25), "400%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 1), "100%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 2), "50%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 10), "10%"), ActionTools.createAction(() -> Commands.setViewerDownsample(viewer, 100), "1%"));
    ToggleGroup groupTools = new ToggleGroup();
    Menu menuTools = MenuTools.createMenu("Set tool", ActionTools.createCheckMenuItem(defaultActions.MOVE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.RECTANGLE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.ELLIPSE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.LINE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POLYGON_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POLYLINE_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.BRUSH_TOOL, groupTools), ActionTools.createCheckMenuItem(defaultActions.POINTS_TOOL, groupTools), null, ActionTools.createCheckMenuItem(defaultActions.SELECTION_MODE));
    // Handle awkward 'TMA core missing' option
    CheckMenuItem miTMAValid = new CheckMenuItem("Set core valid");
    miTMAValid.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), false));
    CheckMenuItem miTMAMissing = new CheckMenuItem("Set core missing");
    miTMAMissing.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), true));
    Menu menuTMA = new Menu("TMA");
    MenuTools.addMenuItems(menuTMA, miTMAValid, miTMAMissing, null, defaultActions.TMA_ADD_NOTE, null, MenuTools.createMenu("Add", createImageDataAction(imageData -> TMACommands.promptToAddRowBeforeSelected(imageData), "Add TMA row before"), createImageDataAction(imageData -> TMACommands.promptToAddRowAfterSelected(imageData), "Add TMA row after"), createImageDataAction(imageData -> TMACommands.promptToAddColumnBeforeSelected(imageData), "Add TMA column before"), createImageDataAction(imageData -> TMACommands.promptToAddColumnAfterSelected(imageData), "Add TMA column after")), MenuTools.createMenu("Remove", createImageDataAction(imageData -> TMACommands.promptToDeleteTMAGridRow(imageData), "Remove TMA row"), createImageDataAction(imageData -> TMACommands.promptToDeleteTMAGridColumn(imageData), "column")));
    // Create an empty placeholder menu
    Menu menuSetClass = MenuTools.createMenu("Set class");
    // CheckMenuItem miTMAValid = new CheckMenuItem("Set core valid");
    // miTMAValid.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), false));
    // CheckMenuItem miTMAMissing = new CheckMenuItem("Set core missing");
    // miTMAMissing.setOnAction(e -> setTMACoreMissing(viewer.getHierarchy(), true));
    Menu menuCells = MenuTools.createMenu("Cells", ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_BOUNDARIES_AND_NUCLEI, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_NUCLEI, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_BOUNDARIES, null), ActionTools.createCheckMenuItem(defaultActions.SHOW_CELL_CENTROIDS, null));
    MenuItem miClearSelectedObjects = new MenuItem("Delete object");
    miClearSelectedObjects.setOnAction(e -> {
        PathObjectHierarchy hierarchy = viewer.getHierarchy();
        if (hierarchy == null)
            return;
        if (hierarchy.getSelectionModel().singleSelection()) {
            GuiTools.promptToRemoveSelectedObject(hierarchy.getSelectionModel().getSelectedObject(), hierarchy);
        } else {
            GuiTools.promptToClearAllSelectedObjects(viewer.getImageData());
        }
    });
    // Create a standard annotations menu
    Menu menuAnnotations = GuiTools.populateAnnotationsMenu(this, new Menu("Annotations"));
    SeparatorMenuItem topSeparator = new SeparatorMenuItem();
    popup.setOnShowing(e -> {
        // Check if we have any cells
        ImageData<?> imageData = viewer.getImageData();
        if (imageData == null)
            menuCells.setVisible(false);
        else
            menuCells.setVisible(!imageData.getHierarchy().getDetectionObjects().isEmpty());
        // Check what to show for TMA cores or annotations
        Collection<PathObject> selectedObjects = viewer.getAllSelectedObjects();
        PathObject pathObject = viewer.getSelectedObject();
        menuTMA.setVisible(false);
        if (pathObject instanceof TMACoreObject) {
            boolean isMissing = ((TMACoreObject) pathObject).isMissing();
            miTMAValid.setSelected(!isMissing);
            miTMAMissing.setSelected(isMissing);
            menuTMA.setVisible(true);
        }
        // Add clear objects option if we have more than one non-TMA object
        if (imageData == null || imageData.getHierarchy().getSelectionModel().noSelection() || imageData.getHierarchy().getSelectionModel().getSelectedObject() instanceof TMACoreObject)
            miClearSelectedObjects.setVisible(false);
        else {
            if (imageData.getHierarchy().getSelectionModel().singleSelection()) {
                miClearSelectedObjects.setText("Delete object");
                miClearSelectedObjects.setVisible(true);
            } else {
                miClearSelectedObjects.setText("Delete objects");
                miClearSelectedObjects.setVisible(true);
            }
        }
        boolean hasAnnotations = pathObject instanceof PathAnnotationObject || (!selectedObjects.isEmpty() && selectedObjects.stream().allMatch(p -> p.isAnnotation()));
        updateSetAnnotationPathClassMenu(menuSetClass, viewer);
        menuAnnotations.setVisible(hasAnnotations);
        topSeparator.setVisible(hasAnnotations || pathObject instanceof TMACoreObject);
        // Occasionally, the newly-visible top part of a popup menu can have the wrong size?
        popup.setWidth(popup.getPrefWidth());
    });
    // popup.add(menuClassify);
    popup.getItems().addAll(miClearSelectedObjects, menuTMA, menuSetClass, menuAnnotations, topSeparator, menuMultiview, menuCells, menuView, menuTools);
    popup.setAutoHide(true);
    // Enable circle pop-up for quick classification on right-click
    CirclePopupMenu circlePopup = new CirclePopupMenu(viewer.getView(), null);
    viewer.getView().addEventHandler(MouseEvent.MOUSE_PRESSED, e -> {
        if ((e.isPopupTrigger() || e.isSecondaryButtonDown()) && e.isShiftDown() && !getAvailablePathClasses().isEmpty()) {
            circlePopup.setAnimationDuration(Duration.millis(200));
            updateSetAnnotationPathClassMenu(circlePopup, viewer);
            circlePopup.show(e.getScreenX(), e.getScreenY());
            e.consume();
            return;
        } else if (circlePopup.isShown())
            circlePopup.hide();
        if (e.isPopupTrigger() || e.isSecondaryButtonDown()) {
            popup.show(viewer.getView().getScene().getWindow(), e.getScreenX(), e.getScreenY());
            e.consume();
        }
    });
// // It's necessary to make the Window the owner, since otherwise the context menu does not disappear when clicking elsewhere on the viewer
// viewer.getView().setOnContextMenuRequested(e -> {
// popup.show(viewer.getView().getScene().getWindow(), e.getScreenX(), e.getScreenY());
// //			popup.show(viewer.getView(), e.getScreenX(), e.getScreenY());
// });
}

Example 5 with ImageData

use of qupath.lib.images.ImageData in project qupath by qupath.

the class BrightnessContrastCommand method createDialog.

protected Stage createDialog() {
    if (!isInitialized())
        initializeSliders();
    initializePopup();
    changed(null, null, qupath.getImageData());
    BorderPane pane = new BorderPane();
    GridPane box = new GridPane();
    String blank = "      ";
    Label labelMin = new Label("Min display");
    // labelMin.setTooltip(new Tooltip("Set minimum lookup table value - double-click to edit manually"));
    Label labelMinValue = new Label(blank);
    labelMinValue.setTooltip(new Tooltip("Set minimum lookup table value - double-click to edit manually"));
    labelMinValue.textProperty().bind(Bindings.createStringBinding(() -> {
        // If value < 10, return 2 dp, otherwise 1 dp. Should be more useful for 16-/32-bit images.
        return sliderMin.getValue() < 10 ? String.format("%.2f", sliderMin.getValue()) : String.format("%.1f", sliderMin.getValue());
    }, table.getSelectionModel().selectedItemProperty(), sliderMin.valueProperty()));
    box.add(labelMin, 0, 0);
    box.add(sliderMin, 1, 0);
    box.add(labelMinValue, 2, 0);
    Label labelMax = new Label("Max display");
    labelMax.setTooltip(new Tooltip("Set maximum lookup table value - double-click to edit manually"));
    Label labelMaxValue = new Label(blank);
    labelMaxValue.setTooltip(new Tooltip("Set maximum lookup table value - double-click to edit manually"));
    labelMaxValue.textProperty().bind(Bindings.createStringBinding(() -> {
        // If value < 10, return 2 dp, otherwise 1 dp. Should be more useful for 16-/32-bit images.
        return sliderMax.getValue() < 10 ? String.format("%.2f", sliderMax.getValue()) : String.format("%.1f", sliderMax.getValue());
    }, table.getSelectionModel().selectedItemProperty(), sliderMax.valueProperty()));
    box.add(labelMax, 0, 1);
    box.add(sliderMax, 1, 1);
    box.add(labelMaxValue, 2, 1);
    box.setVgap(5);
    GridPane.setFillWidth(sliderMin, Boolean.TRUE);
    GridPane.setFillWidth(sliderMax, Boolean.TRUE);
    box.prefWidthProperty().bind(pane.widthProperty());
    box.setPadding(new Insets(5, 0, 5, 0));
    GridPane.setHgrow(sliderMin, Priority.ALWAYS);
    GridPane.setHgrow(sliderMax, Priority.ALWAYS);
    // In the absence of a better way, make it possible to enter display range values
    // manually by double-clicking on the corresponding label
    labelMinValue.setOnMouseClicked(e -> {
        if (e.getClickCount() == 2) {
            ChannelDisplayInfo infoVisible = getCurrentInfo();
            if (infoVisible == null)
                return;
            Double value = Dialogs.showInputDialog("Display range", "Set display range minimum", (double) infoVisible.getMinDisplay());
            if (value != null && !Double.isNaN(value)) {
                sliderMin.setValue(value);
                // Update display directly if out of slider range
                if (value < sliderMin.getMin() || value > sliderMin.getMax()) {
                    imageDisplay.setMinMaxDisplay(infoVisible, (float) value.floatValue(), (float) infoVisible.getMaxDisplay());
                    // infoVisible.setMinDisplay(value.floatValue());
                    // viewer.updateThumbnail();
                    updateSliders();
                    viewer.repaintEntireImage();
                }
            }
        }
    });
    labelMaxValue.setOnMouseClicked(e -> {
        if (e.getClickCount() == 2) {
            ChannelDisplayInfo infoVisible = getCurrentInfo();
            if (infoVisible == null)
                return;
            Double value = Dialogs.showInputDialog("Display range", "Set display range maximum", (double) infoVisible.getMaxDisplay());
            if (value != null && !Double.isNaN(value)) {
                sliderMax.setValue(value);
                // Update display directly if out of slider range
                if (value < sliderMax.getMin() || value > sliderMax.getMax()) {
                    imageDisplay.setMinMaxDisplay(infoVisible, (float) infoVisible.getMinDisplay(), (float) value.floatValue());
                    // infoVisible.setMaxDisplay(value.floatValue());
                    // viewer.updateThumbnail();
                    updateSliders();
                    viewer.repaintEntireImage();
                }
            }
        }
    });
    Button btnAuto = new Button("Auto");
    btnAuto.setOnAction(e -> {
        if (imageDisplay == null)
            return;
        // if (histogram == null)
        // return;
        // //				setSliders((float)histogram.getEdgeMin(), (float)histogram.getEdgeMax());
        ChannelDisplayInfo info = getCurrentInfo();
        double saturation = PathPrefs.autoBrightnessContrastSaturationPercentProperty().get() / 100.0;
        imageDisplay.autoSetDisplayRange(info, saturation);
        for (ChannelDisplayInfo info2 : table.getSelectionModel().getSelectedItems()) {
            imageDisplay.autoSetDisplayRange(info2, saturation);
        }
        updateSliders();
        handleSliderChange();
    });
    Button btnReset = new Button("Reset");
    btnReset.setOnAction(e -> {
        for (ChannelDisplayInfo info : table.getSelectionModel().getSelectedItems()) {
            imageDisplay.setMinMaxDisplay(info, info.getMinAllowed(), info.getMaxAllowed());
        }
        sliderMin.setValue(sliderMin.getMin());
        sliderMax.setValue(sliderMax.getMax());
    });
    Stage dialog = new Stage();
    dialog.initOwner(qupath.getStage());
    dialog.setTitle("Brightness & contrast");
    // Create color/channel display table
    table = new TableView<>(imageDisplay == null ? FXCollections.observableArrayList() : imageDisplay.availableChannels());
    table.setPlaceholder(new Text("No channels available"));
    table.addEventHandler(KeyEvent.KEY_PRESSED, new CopyTableListener());
    table.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    table.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> {
        updateHistogram();
        updateSliders();
    });
    TableColumn<ChannelDisplayInfo, ChannelDisplayInfo> col1 = new TableColumn<>("Color");
    col1.setCellValueFactory(new Callback<CellDataFeatures<ChannelDisplayInfo, ChannelDisplayInfo>, ObservableValue<ChannelDisplayInfo>>() {

        @Override
        public ObservableValue<ChannelDisplayInfo> call(CellDataFeatures<ChannelDisplayInfo, ChannelDisplayInfo> p) {
            return new SimpleObjectProperty<ChannelDisplayInfo>(p.getValue());
        }
    });
    col1.setCellFactory(column -> {
        return new TableCell<ChannelDisplayInfo, ChannelDisplayInfo>() {

            @Override
            protected void updateItem(ChannelDisplayInfo item, boolean empty) {
                super.updateItem(item, empty);
                if (item == null || empty) {
                    setText(null);
                    setGraphic(null);
                    return;
                }
                setText(item.getName());
                Rectangle square = new Rectangle(0, 0, 10, 10);
                Integer rgb = item.getColor();
                if (rgb == null)
                    square.setFill(Color.TRANSPARENT);
                else
                    square.setFill(ColorToolsFX.getCachedColor(rgb));
                setGraphic(square);
            }
        };
    });
    col1.setSortable(false);
    TableColumn<ChannelDisplayInfo, Boolean> col2 = new TableColumn<>("Selected");
    col2.setCellValueFactory(new Callback<CellDataFeatures<ChannelDisplayInfo, Boolean>, ObservableValue<Boolean>>() {

        @Override
        public ObservableValue<Boolean> call(CellDataFeatures<ChannelDisplayInfo, Boolean> item) {
            SimpleBooleanProperty property = new SimpleBooleanProperty(imageDisplay.selectedChannels().contains(item.getValue()));
            // Remove repaint code here - now handled by table selection changes
            property.addListener((v, o, n) -> {
                imageDisplay.setChannelSelected(item.getValue(), n);
                table.refresh();
                Platform.runLater(() -> viewer.repaintEntireImage());
            });
            return property;
        }
    });
    col2.setCellFactory(column -> {
        CheckBoxTableCell<ChannelDisplayInfo, Boolean> cell = new CheckBoxTableCell<>();
        // Select cells when clicked - means a click anywhere within the row forces selection.
        // Previously, clicking within the checkbox didn't select the row.
        cell.addEventFilter(MouseEvent.MOUSE_CLICKED, e -> {
            if (e.isPopupTrigger())
                return;
            int ind = cell.getIndex();
            var tableView = cell.getTableView();
            if (ind < tableView.getItems().size()) {
                if (e.isShiftDown())
                    tableView.getSelectionModel().select(ind);
                else
                    tableView.getSelectionModel().clearAndSelect(ind);
                var channel = cell.getTableRow().getItem();
                // Handle clicks within the cell but outside the checkbox
                if (e.getTarget() == cell && channel != null && imageDisplay != null) {
                    updateDisplay(channel, !imageDisplay.selectedChannels().contains(channel));
                }
                e.consume();
            }
        });
        return cell;
    });
    col2.setSortable(false);
    col2.setEditable(true);
    col2.setResizable(false);
    // Handle color change requests when an appropriate row is double-clicked
    table.setRowFactory(tableView -> {
        TableRow<ChannelDisplayInfo> row = new TableRow<>();
        row.setOnMouseClicked(e -> {
            if (e.getClickCount() == 2) {
                ChannelDisplayInfo info = row.getItem();
                var imageData = viewer.getImageData();
                if (info instanceof DirectServerChannelInfo && imageData != null) {
                    DirectServerChannelInfo multiInfo = (DirectServerChannelInfo) info;
                    int c = multiInfo.getChannel();
                    var channel = imageData.getServer().getMetadata().getChannel(c);
                    Color color = ColorToolsFX.getCachedColor(multiInfo.getColor());
                    picker.setValue(color);
                    Dialog<ButtonType> colorDialog = new Dialog<>();
                    colorDialog.setTitle("Channel properties");
                    colorDialog.getDialogPane().getButtonTypes().setAll(ButtonType.APPLY, ButtonType.CANCEL);
                    var paneColor = new GridPane();
                    int r = 0;
                    var labelName = new Label("Channel name");
                    var tfName = new TextField(channel.getName());
                    labelName.setLabelFor(tfName);
                    PaneTools.addGridRow(paneColor, r++, 0, "Enter a name for the current channel", labelName, tfName);
                    var labelColor = new Label("Channel color");
                    labelColor.setLabelFor(picker);
                    PaneTools.addGridRow(paneColor, r++, 0, "Choose the color for the current channel", labelColor, picker);
                    paneColor.setVgap(5.0);
                    paneColor.setHgap(5.0);
                    colorDialog.getDialogPane().setContent(paneColor);
                    Optional<ButtonType> result = colorDialog.showAndWait();
                    if (result.orElse(ButtonType.CANCEL) == ButtonType.APPLY) {
                        // if (!DisplayHelpers.showMessageDialog("Choose channel color", picker))
                        // return;
                        String name = tfName.getText().trim();
                        if (name.isEmpty()) {
                            Dialogs.showErrorMessage("Set channel name", "The channel name must not be empty!");
                            return;
                        }
                        Color color2 = picker.getValue();
                        if (color == color2 && name.equals(channel.getName()))
                            return;
                        // Update the server metadata
                        int colorUpdated = ColorToolsFX.getRGB(color2);
                        if (imageData != null) {
                            var server = imageData.getServer();
                            var metadata = server.getMetadata();
                            var channels = new ArrayList<>(metadata.getChannels());
                            channels.set(c, ImageChannel.getInstance(name, colorUpdated));
                            var metadata2 = new ImageServerMetadata.Builder(metadata).channels(channels).build();
                            imageData.updateServerMetadata(metadata2);
                        }
                        // Update the display
                        multiInfo.setLUTColor((int) (color2.getRed() * 255), (int) (color2.getGreen() * 255), (int) (color2.getBlue() * 255));
                        // Add color property
                        imageDisplay.saveChannelColorProperties();
                        viewer.repaintEntireImage();
                        updateHistogram();
                        table.refresh();
                    }
                }
            }
        });
        return row;
    });
    table.getColumns().add(col1);
    table.getColumns().add(col2);
    table.setEditable(true);
    table.setColumnResizePolicy(TableView.UNCONSTRAINED_RESIZE_POLICY);
    // Hack... space for a scrollbar
    col1.prefWidthProperty().bind(table.widthProperty().subtract(col2.widthProperty()).subtract(25));
    // col2.setResizable(false);
    // col2.setMaxWidth(100);
    // col2.setPrefWidth(50);
    // col2.setResizable(false);
    // col1.prefWidthProperty().bind(table.widthProperty().multiply(0.7));
    // col2.prefWidthProperty().bind(table.widthProperty().multiply(0.2));
    // table.getColumnModel().getColumn(0).setCellRenderer(new ChannelCellRenderer());
    // table.getColumnModel().getColumn(1).setMaxWidth(table.getColumnModel().getColumn(1).getPreferredWidth());
    BorderPane panelColor = new BorderPane();
    // panelColor.setBorder(BorderFactory.createTitledBorder("Color display"));
    BorderPane paneTableAndFilter = new BorderPane(table);
    TextField tfFilter = new TextField("");
    tfFilter.textProperty().bindBidirectional(filterText);
    tfFilter.setTooltip(new Tooltip("Enter text to find specific channels by name"));
    tfFilter.setPromptText("Filter channels by name");
    paneTableAndFilter.setBottom(tfFilter);
    predicate.addListener((v, o, n) -> updatePredicate());
    panelColor.setCenter(paneTableAndFilter);
    CheckBox cbShowGrayscale = new CheckBox("Show grayscale");
    cbShowGrayscale.selectedProperty().bindBidirectional(showGrayscale);
    cbShowGrayscale.setTooltip(new Tooltip("Show single channel with grayscale lookup table"));
    if (imageDisplay != null)
        cbShowGrayscale.setSelected(!imageDisplay.useColorLUTs());
    showGrayscale.addListener(o -> {
        if (imageDisplay == null)
            return;
        Platform.runLater(() -> viewer.repaintEntireImage());
        table.refresh();
    });
    CheckBox cbKeepDisplaySettings = new CheckBox("Keep settings");
    cbKeepDisplaySettings.selectedProperty().bindBidirectional(PathPrefs.keepDisplaySettingsProperty());
    cbKeepDisplaySettings.setTooltip(new Tooltip("Retain same display settings where possible when opening similar images"));
    FlowPane paneCheck = new FlowPane();
    paneCheck.getChildren().add(cbShowGrayscale);
    paneCheck.getChildren().add(cbKeepDisplaySettings);
    paneCheck.setHgap(10);
    paneCheck.setPadding(new Insets(5, 0, 0, 0));
    panelColor.setBottom(paneCheck);
    pane.setCenter(panelColor);
    // Create brightness/contrast panel
    BorderPane panelSliders = new BorderPane();
    panelSliders.setTop(box);
    GridPane panelButtons = PaneTools.createColumnGridControls(btnAuto, btnReset);
    panelSliders.setBottom(panelButtons);
    panelSliders.setPadding(new Insets(5, 0, 5, 0));
    BorderPane panelMinMax = new BorderPane();
    // panelMinMax.setBorder(BorderFactory.createTitledBorder("Brightness/Contrast"));
    panelMinMax.setTop(panelSliders);
    histogramPanel.setShowTickLabels(false);
    histogramPanel.getChart().setAnimated(false);
    // histogramPanel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    // panelMinMax.setCenter(histogramPanel.getChart());
    panelMinMax.setCenter(chartWrapper.getPane());
    chartWrapper.getPane().setPrefSize(200, 200);
    // histogramPanel.getChart().setPrefSize(200, 200);
    // histogramPanel.setPreferredSize(new Dimension(200, 120));
    pane.setBottom(panelMinMax);
    pane.setPadding(new Insets(10, 10, 10, 10));
    Scene scene = new Scene(pane, 350, 500);
    dialog.setScene(scene);
    dialog.setMinWidth(300);
    dialog.setMinHeight(400);
    dialog.setMaxWidth(600);
    dialog.setMaxHeight(800);
    updateTable();
    if (!table.getItems().isEmpty())
        table.getSelectionModel().select(0);
    updateDisplay(getCurrentInfo(), true);
    updateHistogram();
    updateSliders();
    // Update sliders when receiving focus - in case the display has been updated elsewhere
    dialog.focusedProperty().addListener((v, o, n) -> {
        if (n)
            updateSliders();
    });
    return dialog;
}