--- updatedAt: 2025-08-31T10:34:44.000Z agentTools: projectIndex: https://docs.sparc.science/llms.txt --- # Adding Fiducial Markers and Groups How to add fiducial markers and groups to an organ scaffold ## Step 1: Create and execute a workflow For this task, we will be demonstrating how to add user-defined fiducial markers and annotation groups to an organ scaffold. This step is usually performed to improve alignment and fitting of the scaffold to segmentation data. To start we [Create a Skeleton Dataset Structure](https://docs.sparc.science/docs/scaffold-mapping-tools-mapping-creating-skeleton-dataset-structure). Launch MAP Client Mapping Tools, found in the Start Menu under [MAP-Client-mapping-tools vX.Y.Z](https://docs.sparc.science/docs/map-scaffold-mapping-tool-installation-guide) (The X, Y, and Z will be actual numbers depending on the current stable release). You can create a new workflow anywhere but here we will create one on the Desktop. Using Windows explorer, or similar, create a new directory on the Desktop and name it Add Fiducials. From the File menu in MAP Client Mapping Tools select the New workflow (CTRL-SHIFT-N) to start a new workflow. Navigate to the Desktop and select the Add Fiducials directory created earlier. In this example, we will create a simple workflow to demonstrate the steps of adding fiducial markers and groups. The techniques described here can be adapted for any mapping workflow and integrated in the scaffold creation step. Add **Scaffold Creator** and **File Location Sink** to the workspace and link **Scaffold Creator** to **File Location Sink**. Click on the green wheel icon on **File Location Sink** and change the **identifier** field to **output** and select the output directory. Figure 1. Workflow showing connections for scaffold creation. After setting up the workflow as shown in Figure 1, save the workflow (CTRL-S) and execute the workflow (CTRL-X) by pressing the **Execute** button in the lower right corner of the application main window. ## Step 2: Select a scaffold At the Scaffold Creator interface, select **3D Box 1** under the **Scaffold type** and set the **Number of elements 1**, **Number of elements 2**, and **Number of elements 3** to **2**. Check the box next to **Marker points** as shown in Figure 2 to enable display of marker points after they are created. Figure 2. Scaffold Creator configured for a 3D box scaffold with 8 elements, with marker points turned on to display markers. ## Step 3: Add a user-defined fiducial marker Go to the **Annotation** tab. Click on the **New marker** button and the **Group** field will automatically be populated as group1. A marker point named **group1** is now created and displayed at the origin of the axis. This new marker can be customized by renaming **group1** to **marker1** under the Group field. If you would like to add an ontology identifier for the marker, you can enter the identifier under the **ONT :ID** field. Figure 3. Addition of a new user-defined marker. The marker location can be adjusted via two methods. If - is set for the **Material coordinates field**, the marker location can be set using the element number and element xi under the **Element** field and **Element xi coordinates**, respectively as shown in Figure 4. Figure 4. Setting marker location using element and element xi. Next, add a new marker and rename it as **marker2**. We will use **marker2** to demonstrate an alternate way to adjust the location of the marker. As shown in Figure 5, select **coordinates** under the **Material coordinates field**. Now, the marker location can be set using its coordinate values under the **Material coordinates field**. As this 3D box is of unit scale, setting **0.5, 0.5, 0.5** moves **marker2** to the middle of the 3D box scaffold. Figure 5. Setting marker location using coordinate values. ## Step 4: Add a user-defined annotation group Apart from fiducial markers, we can also create higher dimensional annotation groups for 1D lines, 2D surfaces and 3D volumes. First, make sure that no group is selected under the **Group** field. We then select the graphics for objects of the required group on the graphic window. Press the **S** key and use the left mouse click to select objects for the group you wish to create. When doing selection, make sure that the first click is in the graphic display window to give it focus, otherwise the character **S** could be entered as a parameter or part of the group name. To select multiple different objects (note that objects in a group must be of the same dimension), hold on to **Shift+S** while selecting with the left mouse. Box selection is also available by dragging the mouse, provided the initial click is away from any objects. Selecting a blank area of the screen clears the selection. Here, we have selected a 2D surface (highlighted in red in Figure 6). Go to the **Annotation** tab, click on the **New** button and a new group called **group1** will be created automatically. Next, rename **group1** to **surface1** under the **Group** field. Note that the **Dimension** field will automatically pick up the highest dimension of the selected objects (in this case, 2 as we have selected a surface). A group will be created for its highest dimension, plus their lower dimensional components. We can check if the group is created correctly by toggling the drop down list under **Group** to another group (for example, **marker2**) and selecting **surface1** again from the list to make sure that the correct elements for the group **surface1** are highlighted in red on the display panel. Figure 6. Adding a new user-defined annotation group. Once an annotation group is created, it can also be redefined by reselecting the elements for the group using the **S** or **Shift+S** key, followed by choosing the specific annotation group from the drop down list under **Group**, selecting the **Redefine** button and confirming your selection (Figure 7). Figure 7. Redefining selection for a user-defined annotation group. If you wish to delete a user-defined marker or annotation group, select the respective group from **Group** and click on the **Delete** button (Figure 8). Note that the ability to edit and destroy markers and annotation groups is only limited to user-defined annotations. Markers and annotation groups that are already built-in the scaffold cannot be modified or deleted. Figure 8. Deleting a user-defined annotation group. After addition of user-defined fiducial markers and annotation groups, click **Done** or **Next** (if integrated in an image data mapping workflow) to complete the process. Information of the newly created markers and annotation groups will then be propagated to subsequent steps in the mapping process and exported together with scaffold information in the file generated by the workflow. Return to the main [MAP-Core Scaffold Mapping Tools](https://docs.sparc.science/docs/map-core-scaffold-mapping-tools) page.