Getting Started

Getting Started

This page will help you set up and start using u-probe. It first shows you how to launch u-quantify, our software suite, then how to create a MovieData object, and finally how to launch u-probe.

A MovieData is an in-house built data structure that holds links to raw images, original metadata, stored links to analysis results, and parameters utilized for image processing. It keeps raw data separate from analysis and provides flexibility to re-run analyses with different parameters without altering the original data.

📺 Video guide: How to Create the MovieData (YouTube tutorial)

Launching u-quantify

To launch the u-probe software, type below command in the MATLAB command window:

u_quantify()

Then click "new". This will open another “Movie edition” window.

Create the movie data using the Bio-Formats importer

If the data follows the Bio-Formats standard, you can create the movie data using the Bio-Formats importer option. You will need to specify the output path first. Then, click the “Import movie using Bio-Formats” button to select the Bio-Formats movie file. Some of the metadata will be automatically imported, but you can still manually input some parameters for the movie.

Click “Save”. Now the movie data .mat file has been created and saved in the output folder. Using this method, the name of the movie data will be the same as the Bio-Formats movie file.

Now, you can click "Continue" to launch the "u-probe" application.

Create the movie data using the channels option

This option allows you to setup a movie data by selecting folders containing the images for each channel of the movie. Each channel (wavelength) must be in a separate folder, with one file per frame (a single tiff file per time point). Note that all channels should have the same number of images, and their images should all be the same size.

In the “Channels’ panel, click “Add channel”. Then click the folder of channel one, click “Select Folder” to add channel. You may add other channels the same way. On the right on the "Movie Information" panel, you can input the parameters for this movie, such as Pixel Size, Time Interval, or Camera Bit Depth. Metadata is usually optional but can be required by some analysis packages. You will also need to specify the output path.

Click “Save”. You can give a name for this movie data. The default name is movieData.mat. Now, the movie data .mat file has been created and saved in the output folder.

Now, you can click "Continue" to launch the "u-probe" application.