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Tutorials

The tutorials were written with a purpose to provide step by step how to use all the basic functionalities of MARS-ALT.

As MARS-ALT is currently based on Linux environment, the tutorials are mainly a guide through some basic bash scripts.

Through the tutorials, some bash scripts call binairies which are available with MIPS.

MARS

A quick guide through MARS showing the basic steps to 3-D reconstruction and segmentation of volumetric images

Building MARS environment and Converting : Generating groups of shell scripts and work folders in order to get starting with MARS and converting of input data (series of 2-D image files) into an optimized 3-D image format named inrimage.

User-guided linear registration : Registration of images based on manually identification.

Automated linear registration : Rigid registration computed from mapping between blocks.

Automated non-linear registration : Registration computed from block-based pyramidal algorithm.

Fusion : Iterative Fusion.

Segmentation : Automated cell segmentation.

Using of TIFF images : Converting TIFF images into InrImage.

ALT

Using of ALT : A guided tour through the tracking cell lineages during growth.

VIS : Tool for visualizing segmentation results

VIS : Using the visualisation software.