Online course

The course took place online via Zoom on December 13th-16th at 14:00-16:00 Central European Time (UTC+1).

The course covered:
-How to generate a mesh and project the signal from confocal images.
-Cell segmentation in 2.5D and 3D.
-Quantification of cell geometry and fluorescence.
-Manual and semi-automatic parent labelling.
-Generation of growth heatmaps and principal directions of growth.
-Creation of custom coordinate directions and distance heatmaps.
-Creation of morphing animations between timepoints.
-Automatic recognition and classfication of cell types.

Each section was followed by practicals in which participants tried first-hand the processes.


MorphoGraphX has now joined the scientific imaging forum. For help and discussion on MorphoGraphX please use’t forget to tag your posts with “MorphoGraphX”.

Follow us on Twitter

Check out our Youtube Channel


All the most recent versions of the documentation can be accessed in from the “help” menu of the MorphoGraphX window. It contains the following documents:

  • User manual: The user manual is written in tutorial-style, and is based on published exemplary data that can be downloaded here. The manual can be used as an introduction to MorphoGraphX for novices, e.g. how to install the software, optimize data collection for MorphoGraphX analysis and run the most popular processes. It also contains information useful to more advanced users, such as troubleshooting for common problems or installation of plugins.
  • Process Reference: Each process comes with a description of its use and of its parameters, contained in the source code. These “tooltips” are accessible from the MorphoGraphX window, by placing the mouse cursor over the process or parameter name. A list of all the processes and their descriptions is also available under the software “help” menu (“Process docs”). This document is generated on the fly and is always tied to the version of MorphoGraphX currently installed on your computer.
  • Doxygen documentation: a description of the processes parameters and classes used in the source code is available for developers. Go to the “help” menu in the user interface. Example of plugins are also available. 

Frequently Asked Questions (FAQs)

MorphoGraphX is installed but does not work?

First check the troubleshooting section in the installation section of the manual. The most common problem is that the nVidia graphics driver or Cuda is not installed properly on your computer. On Linux, be sure you have a recent enough driver to support your nVidia graphics card. Packages were compiled with Cuda 11.4, and although not strictly required to run MGX, installing Cuda 11.4 will install the correct nVidia driver.

Some AddOns require optional libraries, and will not load if these libraries are not installed. If this happens, you can see the error in the terminal window.

Can MorphoGraphX run on a laptop?

Yes, and if it has an nVidia card, you can use the Cuda version.

I can’t select anything with the Alt key.

By default Ubuntu uses the Alt key to move windows around, preventing it from being used for selection in MorphoGraphX. You can change this to the “Super” key, which has a windows sign on it on many keyboards. This is done in the windows settings in Linux, and the procedure varies in each distribution. It is usually called the modifier key.

I loaded my stack but it is not visible, why?

If your image stack is stored in 8 bits instead of 16 bits, the data will be too dark to see. You can auto-adjust the transfer function to visualize your data. If it is a labelled stack, such as a segmentation imported from another software, be sure labels is turned on.

Can any confocal stack be analyzed in MorphoGraphX?

Yes, however the results can depend a lot on the image quality. For highly curved samples, the stack needs to have a very fine Z step. You will find microscope tips to optimize data collection in the manual.

Why doesn’t MorphoGraphX’s terminal (small black screen) disappear immediately when I close the window?

The terminal is used to print out information and error messages. This helps us testing the software and tracking down bugs that cause MGX to crash, as it gives some time to read the error messages before the crash. In case of problems, please copy the messages and send them to us.

Do I need a python environment to install the CNN AddOn

No, the CNN tiler uses TorchScript and is fully implemented in C++.

How can I use a trained model in MorphoGraphX?

To use a model in MorphoGraphX, it needs to be traced into TorchScript to generate a .pt file. If you have a trained network that you would like to share, please let us know and we’ll add it to our model library.

Helpful Videos

The MorphoGraphX GUI
How to use CCN AddOn
Tracking cell lineage in MorphoGraphX
Auto segmentation of cells on surfaces
Surface extraction and segmentation
How to split and combine cells
%d bloggers like this: