Top


Introduction

The measurement tool in OMERO.insight is used to draw Regions of Interest (ROIs) and perform some basic analysis.

OMERO.web allows you to view existing ROIs, but not edit them or create new ones.


Drawing ROIs

  1. Open the image in the Image Viewer and click on the Measuring Tool icon to open the tool palette.


    ../images/measurementToolIcon.jpg

  2. Use the ROI selector icon to select ROIs for analysis, resizing, reshaping or moving on image.

    Select the appropriate tool to draw rectangular, ellipse, point, line or polygon ROIs.

    Text ROIs can be added with the text tool.


    ../images/measurementToolToolbar.jpg

  3. Click on the Rectangle or Ellipse icons in the tool bar to draw a rectangular or elliptical ROI.

    Use the corners or edges to resize the ROI.

    Use the selection tool to move ROI on image.

    Double-click on the ROI to add a label to the ROI.

  4. Use the Show Comment checkbox in the toolbar to toggle labels on and off.


    ../images/measurementToolShape.jpg


  5. On elliptical ROI’s click on and drag the green dot at the top to rotate the ellipse.


    ../images/measurementToolEllipse.jpg

  6. Double-click on a line ROI to insert an additional point into the line.

    ../images/measurementToolLine.jpg



  7. Ctrl-click (Windows) or Cmd-click (Mac) changes the type of a point.

    The default type is an edge point, with collinear control point, unconstrained control point and quadratic curve point the other options.

    Point types other than the default edge point, have Bezier controls that allow the line adjacent to the point to be curved as needed e.g. to pass through specific structures.

    ../images/measurementToolPoint.jpg


  8. Click the Polygon icon, click on the image, and then click again to start drawing a polygon ROI on an image.


  9. Right-click on any ROI to use the contextual menu to perform the operations available.


    ../images/measurementToolContextual.jpg

  10. Click on the Save icon to save ROIs.


    ../images/measurementToolSave.jpg

  11. Click on the Upload icon to upload ROIs from an external file.


    ../images/measurementToolUpload.jpg

  12. Click the Delete button to delete all ROIs on an image.

    Right-click on an individual ROI and select Delete to delete only a single ROI.

    Select multiple ROI’s, right-click and select **Delete** to delete those ROIs.


    ../images/measurementToolDelete.jpg



ROI Folders

ROI Folders provide a way of grouping ROIs on an image or across images for the purposes of organisation, analysis or visualisation. ROI Folders support hierarchies, so can contain both other folders and ROIs.


Note

There are still some permissions issues in OMERO.insight meaning that at present, even in groups where the permissions should allow this, you cannot add ROIs created by other people to Folders. If you are comfortable using the Command Line Interface, you use that instead and OMERO.insight will then display the Folder contents correctly.

  1. ROIs and folders are shown in the Manager tab of the Measurement Tool.

    By default only folders containing ROIs on the image being viewed are shown.


    ../images/measurementToolFolderOpen.jpg

  2. Select one or more ROIs to add to a folder.

    Right-click on the selection and choose Create Folder from the menu.

    Type the name and any description into the text boxes.

    Click Create.


    ../images/measurementToolFolderCreate.jpg



  3. Click the Add ROI Folders button to add an existing folder to the Manager display.

    In the Add to ROI Folders dialog, select available folders in the left pane.

    Type in the text box above the Available pane to filter the ROI Folders shown.

    Click the blue arrow to add them to the Selected pane on the right.

    Click Save to add the folders to the Manage display.


    ../images/measurementToolFolderAdd.jpg



  4. Use the drop-down menus below the pane, to refine the search parameters by selecting Anywhere in the name or Start of the name, All, Owned by me, or Owned by others from the menus.

    Create a new folder by typing the name in the text box at the bottom of the window, add any description, and clicking Add.

    Click Save to add the folders to the Manage display.


    ../images/measurementToolFolderAddNew.jpg

  5. In the Manager tab of the Measurement Tool, use the Filter ROI Folders text box to filter the folders displayed.

    Folders owned by other users have the shared flag on them.


    ../images/measurementToolFolderFilter.jpg



  6. Right-click on a ROI and select Add to Folder to add the ROI to an existing or new folder.

    On opening, the Add to ROI Folders dialog will only show folders currently displayed in the Management Tab.

    Use the Filter ROI Folders text box to filter by folder name.

    Click on the Source drop-down and select the All Folders option to display all the folders in the system.


    ../images/measurementToolFolderAddTo.jpg

  7. Drag and drop a ROI onto a folder to add it, or out of a folder to remove it.

  8. Right-click on a ROI within a folder and select Remove from Folder to “orphan” a ROI.


    ../images/measurementToolFolderRemove.jpg


  9. Right-click on a folder within another folder and choose Move Folder from the menu to move a folder and its contents to another folder or to “orphan” it.

    Select a folder or None in the Destination Folder window.

    Click OK.


    ../images/measurementToolFolderMove.jpg

  10. Deselect or select the Show checkbox to hide or show folders or ROIs.

    A change in the state of the Show checkbox for a folder is also applied to the contents of the folder.


    ../images/measurementToolFolderShow.jpg

Note

All these operations can be performed on multi-selected objects.



Propagating ROIs

  1. Any ROI drawn will be on the currently viewed Z section and time point.

    Click on the ROI Assistant icon to propagate an ROI across Z sections or time points.


    ../images/measurementToolAssistant.jpg

  2. In the ROI Assistant window, click on the ROI and drag it.

    Up or down propagates through the Z sections.

    Drag left or right to propagate through the time points (T).

    Dragging diagonally will propagate the ROI through both Z sections and time points.

    Click Close to return to the ROI palette.


    ../images/measurementToolDrag.jpg

  3. Click the Remove ROI radio button and click and drag on ROIs to remove them from Z sections or time points.


    ../images/measurementToolRemove.jpg



Managing and analysis

  1. Details of ROIs are viewed in the **Manager** tab of the tool palette.

    The columns show:

    - ID of the ROI

    - Z sections and time points the ROI is drawn on

    - ROI type

    - text associated with the ROI

    - check box to toggle the visibility of the ROI.


    ../images/measurementToolManager.jpg

  2. Select an ROI and click on the Inspector tab to view and edit the text label, dimensions, fill and line color, and toggle the visibility of the text and measurements on and off.


    ../images/measurementToolInspector.jpg


  3. Click on the Graph Pane tab to show a plot of the channel intensity values for an ROI.

    A line ROI has a profile of intensity values along the line and a histogram of intensity vs. frequency (other types of ROI show only the histogram).

    If an ROI is propagated across Z sections or time points, the sliders to the left of the histogram allow stepping through the sequences.


    ../images/measurementToolGraph.jpg

  4. Click on the Intensity View tab to see tables of intensity values for the ROI.

    >These values can be exported in Excel format for further analysis.


    ../images/measurementToolIntensity.jpg

  5. Click on the Intensity Results View tab to see tables of intensity values for the ROI.

    Click Add Selected to show results for the selected ROI.

    These values can be exported in Excel format for further analysis.


    ../images/measurementToolResults.jpg


  6. Viewing ROIs in OMERO.web

    ROIs cannot be drawn in OMERO.web, but can be viewed, along with basic line plot of channel intensity values.

    1. Open the image in the Full Viewer.

      Click the Show ROIs link at the bottom of the toolbar.

      The ROIs palette opens in the top left corner.

      Toggle visibility on and off using the checkboxes.


      ../images/measurementToolWeb.jpg

    2. Click on the Expansion Arrow on propagated ROIs to show the shapes on Z sections or time points.


      ../images/measurementToolExpand.jpg


    3. Click the Line Plot check box to show a line plot on the image.


      ../images/measurementToolLineWeb.jpg

    4. Select orientation from the Axis drop-down.

      Click Apply.


      ../images/measurementToolExpand.jpg

    5. Enter the desired X or Y coordinate in the text box and click Apply or click on a point in the image to set the line plot position.


      ../images/measurementToolOrientation.jpg


    All Tutorial Material is available on line at: help.openmicroscopy.org

    The Main OME website is at: www.openmicroscopy.org