Skip to content

Running AutoTube from source code

Jump to bottom
autotubularity edited this page Sep 21, 2018 · 7 revisions

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

  4. To validate that AutoTube is running smoothly, you can process one test image. To do so, download the test image named test_image.tif from the following link: https://goo.gl/SdetUu. Store the image locally to your hard drive. Note that also the automatic results from AutoTube are going to be stored in this directory. In the example below, the .tif image was downloaded into the MATLAB directory under Documents.

  5. In the AutoTube GUI click "select folder" (No. 1 in the Figure below) to choose the directory containing the image, in our example /Documents/MATLAB". Next, adjust the "input color channel" to red (No. 2 in Figure) and set the "remove small regions" value to 0.2 (No. 3 in Figure). To run the analysis, click on the button "Analyze" (No. 4 in the Figure below).

Clone this wiki locally