LithoGraphX 1.2.0 documentation
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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

Table Of Contents

  • 1. Installation
  • 2. Principles and user Interface
  • 3. Tips for Data Collection
  • 4. Tutorials
    • 4.1. Loading and visualizing data
    • 4.2. Data Visualization (2)
    • 4.3. Segmenting Cells in 3D
    • 4.4. Segmenting Cells in 3D (advanced)
    • 4.5. Segmenting cells in 2D
    • 4.6. Segmenting cells from a 2D image and automated cell classification
    • 4.7. Computing a growth map
  • 5. Python Macros and Scripts
  • 6. Frequently Asked Questions
  • 7. Writing and Distributing Extensions
  • 8. What’s new?
  • 9. Contributors and Licensing

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© Copyright 2015, Barbier de Reuille, Pierre <pierre@barbierdereuille.net>. Created using Sphinx 1.7.9.