19 Jan Stingray : A Practical Guide
What does it do?
- Stingray is designed to find and classify objects or particles from holograms
- Specifically, Stingray was designed using oceanic phytoplankton samples collected with 4Deep’s instruments. However, Stingray can be used for identification and classification for microorganisms in any liquid environment, including yeast in beverages, or particles in river water quality testing
Why would I use Stingray?
- Stingray will be crucial for anyone who needs to distinguish objects from one another. This includes distinguishing different species within a sample. For example, if a user takes a sample from the ocean, Stingray will be able to group objects into different groups
How does it work?
- First, Stingray analyzes holograms, which are 2D images that contain 3D information. Essentially, a hologram contains information in a volume, so think of a hologram as a cube (or a cone/pyramid). Stingray cuts through the volume in slices or planes (the number of slices is inputted by the user) and checks to see if there are any particles in the plane. If the particle meets the criteria (again, inputted by the user), it is added to the database as an object
- These particles are then sorted into groups or taxon manually by the user
- Good particles from these groups are then used to train a classifier. Essentially, by telling the classifier these are taxon A and these are taxon B, it can differentiate between two taxon
Database: located in the main window, it holds all of the objects that Stingray extracts from holograms
Object: loosely refers to any particle selected by Stingray that is added to the database
Taxon: group. It does not have to be species specific, it can be as simple as “good particles” and “bad particles” or “circle” and “rod”. Essentially it is a sorted object
Sample: an object that has been assigned a taxon and will be used to train classifiers
Classifier: the algorithm that is trained by samples. The classifier will sort objects into taxon
|1. Get some Holograms||
|2. Get Objects from Holograms||
|3. Sort Objects into groups
TIP: Create a “Noise” particle group for out-of-focus particles
|4. Pick Objects to Train Stingray||
TIP: You can stop training if it is failing or if it has passed instead of waiting until the end
|6. Use Classifier on Objects
TIP: You may need more than one classifier