The Twin Slicer

The Twin Slicer is a Volume Visualization tool for 3D microscopy data, which is available in Huygens Essential and Huygens Professional. It works also in FreeWare mode, without a License String.

The Twin Slicer allows you to synchronize views of two images, measure distances, plot line profiles, etc. In Basic Mode (also available without a license), image comparison is intuitive and easy, while the Advanced Mode gives the user the freedom to rotate the cutting plane to any arbitrary orientation, link (synchronize) or unlink viewing parameters between the two images, and more.

To launch the Huygens Twin Slicer, select an image and choose 'Twin Slicer' from the 'Visualization' menu in the main menu. To view another image in an existing slicer, click the image name in the drop-down menu above the displayed slice.

Raw (right) and deconvolved (left) versions of an image can be easily compared in the TwinSlicer
Raw (right) and deconvolved (left) versions of an image can be easily compared in the TwinSlicer


Click and hold the middle mouse button on the slice to move it around. Clicking the Center (Image ) button or pressing 'c' centers the slice.


Drag the slider beneath the displayed slice to move the cutting plane back and forth. This can also be achieved using the buttons adjacent to the slider (Image and Image ), the up/down arrow keys on the keyboard, or by placing the mouse pointer over the slider and using the scroll wheel. The play button moves the cutting plane through the data volume. The pointer coordinates can be displayed through the 'View' menu.
Note that it is possible to move the cutting plane out of the volume. Pressing the Center button (Image ) or the 'c' key centers the plane again.

Changing time frames

Drag the slider in the 'Time frame' panel to change the time frame or press the play button to animate the time series. The time frame can be displayed through the 'View' menu.


Make a selection in the 'Orientation' panel to change the plane used to display the image.


Click the buttons in the 'Zoom' panel or use the scroll wheel to zoom in or out on the location of the mouse pointer.

Selecting Channels and changing display colors

Channels can be (un)selected for display.
Click an option in the 'Colors' panel to select a color scheme:
  • Greyscale. The image is displayed in gray tints. For single-channel images, this gives a higher contrast than the emission or global (default RGB) colors.
  • Emission colors. If the the emission wavelengths are set correctly, this gives the most intuitive view.
  • Global colors. Colors as defined in the Options for channels 0, 1, 2, etc. (by default: red, green, blue, ... respectively)
  • False colors. A false color is given to each intensity value. This view gives a high contrast and makes it easy to spot areas of homogeneous intensity.
  • Custom colors. Use the color picker to manually select a color for each channel.

Tuning the brightness and contrast

You can adjust the brightness in the 'Brightness' panel using the buttons (Image and Image ), dragging the slider, or putting the mouse pointer over the slider and using the scroll wheel.
The 'Gamma' drop panel provides you with a linear and some non-linear ways of mapping data values to pixel intensities. If the 'Link channels' box is checked, this means that the way of mapping data values to pixel intensities is the same for all channels; if not, the range is automatically adjusted for the minimum and maximum in each channel. This range can either be adjusted globally (the complete data set will be taken into account), or for each screen view.

Linking, View & Plot

Here are options listed that can also be found in the menu's. For more information, we refer yo to the manual and tutorials (see links below).


Allows you to set the frame rate in frames per second for creating animations through time or through the Z stack.

Automatic panning, slicing and zooming

When you click with the right mouse button on the scene, a menu will appear with the following options:
zoom in brightest spot. The image will zoom in on the brightest spot in a 3D area close to the cursor.
Fit in canvas. Fits the view in the canvas
Show actual image size. Fits the image with the size of your screen pixels. In other words. the real sizes of the object(s) is shown on your monitor.
Center image. Centers the image in the canvas.
Set marker. Sets a marker that shows the corresponding voxel coordinates and the voxel intensity of each channel.

More information

For more information on
  • Automatic panning, slicing and zooming
  • Measuring distances and intensity profiles
  • The data plotter
  • Viewing modes
please read the Twin Slicer Basic Tutorial and the Twin Slicer Advanced Tutorial.