4.2. Data Visualization (2)

Shoot apical meristem of A. thaliana

Figure 1: Shoot apical meristem of A. thaliana, cell walls stained with PI and with DR5::YFP fluorescent marker. Image: Agata Burian

4.2.1. Introduction

The purpose of this exercise is to introduce the interface of LithoGraphX, learn to segment cells in 3D and work with the heat map.

Note that you will find a lot of useful information in the Help menu, including a user manual, a documentation of all the existing processes, and the mouse and keyboard interactions.

LithoGraphX has a fixed number of objects that exist at any given time. They are organized in two Stacks, each stack containing two images and a mesh. The stack defines the size, resolution and position of the images it contains. The two images are called the Main and Work store: the main store is where the data is loaded by default, while the work store is where the result of any processing will be put. Only one store can be active at any given time. Which is active depends on the visibility of the stores and which stack tab is currently active. It is however, indicated on the right of the status bar, at the bottom of the main window.


In the beginning, always check which store is active before launching processes.

Each stack also contains a triangular mesh. To each vertex of the mesh is attached a signal and a label. The label however, is interpreter by triangle: if at least two vertices of a triangle have the same label, the whole triangle is given this label. In case of tie, the triangle is considered un-labelled. At last, to each label a heat may be associated. A mesh can be seen either as a continuous surface, displaying the signal, label or label’s heat, or as a wireframe mesh, or both at the same time.

In LithoGraphX, loading, saving, processing, analysing is done through Processes (in fact, most menu items are simply shortcuts to processes). There are three kind of processes: Stack, Mesh and Global. Stack processes can only modify the stacks and stores, the Mesh processes can only modify the meshes and Global processes can modify anything.

4.2.2. Loading a stack

Once LithoGraphX is started, the simplest way to open a new image stack is to drag&drop the file (tif) onto the drawing area. You can also use the Stack menu to open a file to a particular store.

4.2.3. Loading a second channel

To load a second channel, you can either use the menus, or again drag&drop a file. However, instead of dropping onto the drawing area, you can drop the file onto the Work store area (see Main tab).

4.2.4. Clipping planes

Clipping planes

You should now have a nice image the SAM, But you cannot easily see inside! To help with this, LithoGraphX has few tools. The first one is three pairs of clipping planes (see Figure~ref{fig:clipping}). To work with the clipping planes, they must be enabled in the View tab. Each pair of clipping plane has its own tab, from which the user can enable it, show a grid to see its position when not enabled, and set the distance between the two planes. To move the planes, it must be selected in the main tab in the Control-Key Interaction box. As the name suggest, the clipping planes are then moved by pressing the Control key and use the mouse in the same way as for moving the camera.

Try using the clipping planes to see where the DR5::YFP signal is with respect to the cell layers.

4.2.5. Cutting Surfaces

Cutting surfaces

Another way to see the insides of a volume is to use cutting surfaces. Like the clipping planes, the cutting surface need to be enabled in the View tab, at the bottom. The cutting surface can take one of three forms: a single plane, three orthogonal planes, or a Bézier surface. When enabled, the part of the visible volumes that intersect the chosen surface will be drawn, ignoring their brightness and opacity settings. Instead, the brightness and opacity of the surface is usedfootnote{To see a volume only on the cutting surface, push its opacity slider all the way to the left, making it completely transparent.}.

As for the clipping plane, you can move the cutting surface is it is selected in the Control-key interaction box.

At last, for the Bézier surface, if you show the grid and make sure points are shown, you can select and move them using the mesh selection tool.