This post contains all the code (or links to code/programs) that you will need for BOS processing. This post accompanies my YouTube video on the subject, which I recommend you watch. If you would rather read, I have a comprehensive PDF document on the topic as well (it is too big for GitHub, so you can find it at my website). All of these files can also be downloaded from my website.
There are some free programs you will need for this project. Below is a comprehensive list of those used in my video.
If you are running my Python GUI program, you will also need to download the following function file.
Again, all the files can also be found on my website.
- If you are running this program on a Mac and get an error, there is a good chance it's because of the difference between Windows and Mac when it comes to folder/directory naming. Try switching all the slashes in the directory name to "/". For instance, one location where you'll need to change it in the MATLAB code is in the pushSelectVideoDirectory_Callback function callback.
- As of 01/16/21, a new version of the ImageJ script for saving a sequence of images is available. If you are using the most up-to-date ImageJ version, you should download BOS_Save_Sequence_v2.ijm. If you want to make this script available automatically every time you open ImageJ (without having to install it every time), add the code in the script to the file called StartupMacros.fiji.ijm (the startup macro script for FIJI/ImageJ). This should be located in the macros folder of your installation. You'll need to copy-paste the code from BOS_Save_Sequence_v2.ijm in between the braces of the code shown here:
macro "BOS Save Sequence 2" {
}
- An updated version of the MATLAB code (GUI_BOS_v3.m) was uploaded on 01/17/21, which works with the new filenames from the updated ImageJ macro (BOS_Save_Sequence_v2.ijm). Note that this updated code only affects the video processing, not the image processing.