=== For regenerating mipmaps the fastest possible ===
In TrakEM2 0.9a and later, the mipmaps machinery
uses a multi-threaded Gaussian implementation now present in the latest ImageJ. This means that now there are two sets of threads:
If your machine has 12 cores, the default settings will use
12 threads for mipmaps and 12 threads for gaussian blurring. This means that, if you are regenerating 12 or more images, there will be 12 + 12 * 12 = 156 concurrent threads. That's too many threads.
You must decide between two strategies:
<li><b>Strategy A</b>: your data consists of large images (over 4000x4000). Right-click on the TrakEM2 display and choose "Project - Properties...", and set the mipmap threads to 1. Now, mipmaps will be regenerated for one single image at a time, using 12 threads (given 12 cores) for computing the Gaussians.</li> <li><b>Strategy B</b>: your data consists of small images (smaller than 4000x4000). Go to the Fiji window and select "Edit - Options - Memory & Threads...", and set the number of threads to 1. Now, mipmaps will be regenerated for 12 images at a time (given 12 cores), using a single thread for each to compute the Gaussians.</li>
Use <b>strategy A</b> as well if your computer has little RAM, or if access to the images is slow and contentious (such as if the data lives in a USB hard drive).
If you change the method for generating mipmaps to a non-Gaussian method, the above situation does not occur. Set the number of threads for regenerating mipmaps to the number of cores, or less if your computer doesn't have much RAM.