Jerry Sharpe, Computational Biology, Brown University, Week 2

For my second week at the Neretti Lab, I refined my coding skills even more. I was introduced to a software coding package called Cellpose. Cellpose is a deep learning, AI software that is very useful for microscopy analysis on images. Cellpose is a technology that was made to identify and segment objects, such as cytoplasm, membranes, and organelles, in an image of cells. If given an image of hundreds or thousands of cells, one can code using Cellpose to identify and count each individual nucleus within the image, as well as give the area and exact coordinates of each nucleus on a pixel grid. This technology has become very beneficial for analysis. Another thing that makes this program so great is that because it is an AI based software, one can train their own models for recognizing certain objects in images.

For my introduction to coding with Cellpose, I was asked to segment this image of nuclei, each stained with a fluorescent tag. This is the DAPI stained image I was working with.

Here is an image of the coding I used to implement that task.

After running the code on my image, I was able to visualize each outlined nucleus, as well as other functions such as counting and finding position. Here is a visualization of how Cellpose works on the image.

My next step in this project, after segmenting the image, was to take each nucleus and center it on an individual 100 by 100 pixel grid. I’m assuming the next step in this process would be to use another AI model to analyze the nucleus morphology(shape) in order to examine for senescence in the cell.

Another cool thing I got to do this week was present over zoom to the National Institute of Health(NIH) and the Center for Genome Imaging(CGI). This group is an international community of professors and students, dedicating their labs and research to imaging the human genome in super resolution. Being on the zoom call I got to hear about fascinating next gen technology and research that is being implemented in this task. Then I gave a quick presentation regarding the CGI and Neretti Lab’s outreach to the community through my internship, as well an outline of my work with Cellpose.

Outside of the lab has been fun too. On Wednesday, Juneteenth, I had to day off and was able to go to the beach with my roommate and his friends down in New Bedford, MA.

Other than that I have been going to the gym, cooking, exploring the city, as well as biking down the Rhode Island coast on this 20 mile long bike path I found. This image was taken on my ride today.