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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. You can download the process documentation for the current version here
  • 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:

  • 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. You may need to upgrade to Cuda 6.5. On Windows please go to the nVidia website and install Cuda 7.0, which will also install a compatible driver. On either system, if you can get the Cuda samples running then MorphoGraphX should work as well.

  • Can MorphoGraphX run on a laptop?

Yes, but the laptop has to have an nVidia graphics card and you need to get Bumblebee or Primus working.

  • 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 a 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. 

  • 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 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 causing crash before distributing the latest version. In case of problems, please copy the messages and send them to us. 

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