Network datas about MGX

Dear all,
Recently I read a famous research article in eLife named “Topological analysis of muticellular complexity in the plant hypocotyl”. It is very amazing to conduct a topological analysis by using MorphographX. I download its supplement data ,which is an edge list. However I find it difficult to get the data, and I don’t know how to get it.
Could you please give me some advice? Thank you very much!

                                                                                                                   Tai ning

You can do some analysis in MGX itself with the various measures, such as number of neighbors, betweeness centrality and betweeness current flow heat maps (all in Mesh/Measures) from 2D and 3D meshes. You can then export the data to R or Matlab by exporting the attributes maps creates Mesh/Attributes/Export.

You may instead want to export the to a dedicated network analysis tool. In this case you can get the data out of MGX as follows:

  • In 2.5D use Mesh/Export/Save Cell Neighborhood 2D
  • In 3D use Mesh/Export/Save Cell Neighborhood 3D

Dear Richard Smith:
First of all, I am very grateful for your suggestions. The datas such as numbers of neighbors and betweeness centrality are exactly what I wanted. And I finished the 3D segmentation by using the MGX. But I don’t find the “Measure” button in Mesh. Actually, I plan to conduct the network analysis by using a software named Cytoscape. So, I only need to get the edge list by MGX. However, I don’t find the “Save Cell Neighborhood 3D” in Mesh/Export. Is my MGX version too old? I put some photos here thus you can check my MGX. (476.9 KB)
Did I leave out some steps?
Looking forward to your early reply at your convenience.
Best wishes!
Tai ning

Hi Soeren,

Look at the zip they sent, they are using Windows!


Dear Richard Smith,
Yes! I successfully completed a series of operation including 3D segmentation by using windows. To be honest,the software is really amazing!

Hi taining,

Your MGX version is pretty old. We will send you a new one in the next days!
(We are currently preparing a new version to be published on the website, but it might take a a bit more time until it’s ready)

Dear Soeren,
Wow,amazing! Thank you very much! Wish you all the best with the work!
Tai ning