4. Tutorials

You will find here a series of tutorial to accomplish various tasks. Each tutorial is given with a sample dataset and a LithoGraphX task to get you started.

The datasets used in these tutorials can be found there: http://www.lithographx.com/data-gallery

• 4.1. Loading and visualizing data
  • 4.1.1. Loading the data
  • 4.1.2. Tuning the visualization
• 4.2. Data Visualization (2)
  • 4.2.1. Introduction
  • 4.2.2. Loading a stack
  • 4.2.3. Loading a second channel
  • 4.2.4. Clipping planes
  • 4.2.5. Cutting Surfaces
• 4.3. Segmenting Cells in 3D
  • 4.3.1. Loading the data
  • 4.3.2. Cleaning the data
  • 4.3.3. 3D Cells Segmentation
  • 4.3.4. 3D Signal Quantification
• 4.4. Segmenting Cells in 3D (advanced)
  • 4.4.1. Loading the dataset
  • 4.4.2. Extracting the embryo
  • 4.4.3. Segmentation
• 4.5. Segmenting cells in 2D
  • 4.5.1. Extracting the surface of the meristem
  • 4.5.2. Segment the cells
  • 4.5.3. Micro-tubule orientations
• 4.6. Segmenting cells from a 2D image and automated cell classification
  • 4.6.1. Pre-processing
  • 4.6.2. Segmentation of the vascular tissues
  • 4.6.3. Automated cell classification
• 4.7. Computing a growth map