Download 3D Image processing with MorphoGraphX User manual

Table of Contents
User Guide....................................................................................................................................... 4
1. Introduction to MorphoGraphX............................................................................................... 4
Some definitions....................................................................................................................... 4
User interface in MorphoGraphX.............................................................................................4
Main menu, toolbars and “Main” tab....................................................................................... 5
“View” tab................................................................................................................................ 6
“Process” tab.............................................................................................................................7
2. Data collection..........................................................................................................................7
3. Loading samples (stack or mesh)............................................................................................. 9
Troubleshooting......................................................................................................................10
4. Extract the biological object shape.........................................................................................11
Troubleshooting......................................................................................................................12
5. Experiment with Processes.....................................................................................................13
6. Create a 2½D image............................................................................................................... 14
7. Segment the cells....................................................................................................................14
Manual seeding and segmentation..........................................................................................15
Automatic seeding and segmentation..................................................................................... 16
Troubleshooting......................................................................................................................17
8. Refine the subdivision............................................................................................................17
9. Quantify Cell Area................................................................................................................. 18
10. Quantify Fluorescence..........................................................................................................19
11. Parent labeling......................................................................................................................20
Troubleshooting......................................................................................................................22
12. Heat map of growth and cell proliferation...............................................................................22
13. Principal directions of growth (PDGs).................................................................................24
14. 3D segmentation...................................................................................................................28
Troubleshooting......................................................................................................................29