A big part of my role in the Smith Lab has been writing useful tools and applications to make Array Tomography a faster, more automated and more useful tool. Occasionally I come across another lab who can use some of these tools for Array Tomography-related uses or (even cooler) something entirely unrelated.

In case it comes up, I'm a big open source guy so please feel free to use, redistribute, etc.

MultiStackReg v1.4 - Now just drag/drop into your plugins folder! - Prior to Array Tomography, our lab had been using Stackreg as an excellent and reliable alignment tool for ImageJ. As we began to image the same tissue repeatedly, we needed to be able to save and load the alignment parameters to ensure that images taken in different sessions were aligned the same way. MultiStackReg is just a slight alteration to Stackreg to allow for save/load functionality.

Array Tomography Toolbar v. 09.10.05 for Axiovision - Array Tomography ribbons have a rather interesting layout that defies most imaging applications. AT sections are laid consecutively on a slide in a mostly predictable fashion, but include too much variation for pure extrapolation to track them. We've developed a method for tracking ribbons using short extrapolations refined by cross-correlation searches. When run, this executable will add a toolbar to your Axiovision installation (you may have to enable it) containing two versions of our tracking algorithm.

The quickest way to get started is to position your camera above a point of interest, press "firstPoint," then move the camera above the corresponding point of the next section and press "secondPoint." The process should be entirely automated from that point, and when it stops you should have a .csv file on your desktop called "Array.csv" You can import this as a position list (see the Axiovision documentation for "Mark and Find") and use it from there. Once you've imaged a position list this way, call "makeStack" to turn the resulting .zva folder into a single volume image.

We're still hashing out the protocol, so if this doesn't work or you need something more, email me and we can talk directly.