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autotubularity edited this page Sep 5, 2018 · 25 revisions

Welcome to the autotube wiki!

This wiki will guide you through the usage of AutoTube. If you use AutoTube, we appreciate it if you cite our paper: Javier A. Montoya-Zegarr, Erica Russo, Peter Runge, Maria Jadha, Ann-Helen Willrodt, Szymon Stoma, Simon F. Nørrelykke, Michael Detmar, and Cornelia Halin. AutoTube: a novel software for the automated morphometric analysis of vascular networks in tissues to be published in the Journal of Angiogenesis.

@article{einstein, author = "Javier A. Montoya-Zegarra and Erica Russo and Peter Runge and Maria Jadhav and Ann-Helen Willrodt and Szymon Stoma and Simon F. Nørrelykke and Michael Detmar and Cornelia Halin", title = "AutoTube: a novel software for the automated morphometric analysis of vascular networks in tissues", journal = "Journal of Angiogenesis", volume = "X", number = "X", pages = "X--X", year = "2018", DOI = "http://dx.doi.org/X/X" }

To allow for AutoTube to be extended or updated we are also providing its source code, which can also be used to run the software directly from the Matlab Console.

To run AutoTube from the source code, you have to download the source code from this repository and store it locally or, otherwise, clone the git repository. After uncompressing/cloning the repository (git clone https://github.com/autotubularity/autotube.git), three directories will be extracted:

Install Step 1

The code directory contains the image processing functions to analyse the images. The gui directory contains the AutoTube graphical interface. Finally, the libs directory contains third-party libraries used by AutoTube. To run AutoTube directly from Matlab, double-click on the AutoTube.m file contained inside the gui directory. Then follow the next steps:

  1. Once Matlab is opened, click on the Run green button on the Editor Toolbox (as shown in the red rectangle in the Figure below): Install Step 2

  2. After clicking on the Run button, the AutoTube GUI is opened and is ready to use. You should get the same Figure below: Install Step 3

Another possibility of running AutoTube from Matlab is to use the guide command from the Matlab Console. To do so, follow the next steps:

  1. Type guide AutoTube.fig in the Matlab Command Window as shown in the Figure below: Install Step 4

  2. The AutoTube.fig GUI is opened. Click next into the Run green button: Install Step 5

  3. The AutoTube GUI is opened and is ready to use. Install Step 6

Note

It is worth to mention that the version of BM3D included in the source code of AutoTube, when running on Linux or Mac OS operating systems, is different than the version of BM3D when running on Windows. The authors of BM3D are going to release officially soon this newer beta version of BM3D for Linux and Mac OS operating systems to solve the current limitations of this denoising tool when running on newer Matlab Versions on the referred operating systems.

As an effort to validate the similarity of our results obtained on Windows using the current official BM3D version (v2.0, released on January, the 30th of 2014) against the results on a Mac OS High Sierra operating system using the forthcoming beta version of BM3D, we analysed the IL-7Ra-/- dataset presented in the Paper in Figure 3 (accessible from: https://doi.org/10.3929/ethz-b-000262426) and report results in Figure 1. More precisely, four different geometrical properties of the lymphatic vessels are compared. They are namely: lymphatic vessel area, skeleton length, vessel width, and number of branching points. Results shown on column A in the Figure depict a good correlation for the analysed geometric properties. In addition, the results shown on column B illustrate the close similarity of both BM3D versions (Windows vs. Mac OS) for both WT and IL-7Ra-/- lymphatic vessels. Note specially that the standard deviation for all four geometrical properties is similar and low.

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