Week 5: Pictures And Videos

Riddle: What goes all around the world but stays in a corner?

Hello everyone and welcome to week 5!!

Pictures And Videos
Alright! For the moment we’ve all been looking forward to… PRETTY PICTURES AND VIDEOS!! Linked below is a video of a Pancreatic Islet. It’s a 3D image comprising a “stack” of 2D images. The image’s different colors represent different proteins stained when processing the islet for imaging. Green is the labeling for the Cell Adhesion Molecule found in epithelial tissue. Red labels the collagen found in the basement membrane that supports epithelial tissues (ie. blood vessels). Blue labels the insulin found in beta cells and white labels the glucagon found in alpha cells.

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This was an Islet that I had annotated a couple of months ago and as you can see, the blood vessels only start halfway through the stack. Interestingly, the blood vessels seem to wrap around the “bottom” or deeper into the stack of images. This feature happens extremely often when multiple blood vessels will merge together while moving through the islet.

Annotations
This is what the Islet looks like after annotation:

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A breakdown of what’s in the video:
There are 3 kinds of annotations, even though the distinction isn’t clear from the video. First, there are annotations that label the cell membrane that is made at the center of the cell membranes. Then, there are annotations that label everything that isn’t a cell membrane. Lastly, there are annotations that label the blood vessels that are made around the blood vessel and associated regions.

Probability Map
Finally, these annotations are processed, resulting in Ilastik creating a probability map.

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Probability maps portray what the classifier thinks is probable to be a certain feature according to the inputted annotations. For example, if we annotate a certain region as being a cell membrane, the classifier will hopefully classify similar regions as cell membranes as well. This probability map is then inputted into Imaris to create a 3D-rendered object that we can then use to analyze. Unfortunately, I don’t have any videos of that :(. I hope this week’s post helped visualize what my project is like and I’ll see ya’ll next week.

Answer: A stamp!!