Week 3: Methodology And Software
March 28, 2023
What can bring back the dead; make you cry, make you laugh, make you young; is born in an instant, yet lasts a lifetime.
Week 3/12. Research is tough and there’s not enough time. I think we all think it’s easy and a lot of research can be easy, but it’s like shooting darts at a board with a blindfold and you don’t even know if you’re facing the board. I’ve been conducting this research since October and this is my mentor’s eighth year of her Ph.D. I think I only feel a sliver of the lostness as my mentor and that’s one of the scary things about research. Are we doing things correctly? Who knows. I guess the reassuring thing is that nobody can tell us that we’re wrong :). Alright, time for the blog.
Methodology
I’ll be analyzing the vascularity of Pancreatic Islets to provide researchers with the information needed to effectively analyze and engineer Islets. So how? The project will utilize 3 main software to analyze images: ImageJ or FIJI which is literally an acronym for FIJI is just ImageJ (who lets researchers name these programs?), Ilastik, and Imaris.
- ImageJ Or FIJI
- ImageJ Is A Program That Helps View H5 Files. H5 Files Are Data Files Saved In The Hierarchical Data Format (HDF) Which Means Absolutely Nothing To Me. Apparently, It Contains “Multidimensional Arrays Of Scientific Data” Which Makes Sense Because, For My Project, It Stores Data For 3D Images. ImageJ Helps Visualize The 3D Images Of Islets In Different Planes (XY, XZ, YZ Planes). FIJI Will Aid In The Visualization Of The Islet Because While The Next Software Helps, It’s A Bit Slow.
- Ilastik
- Ilastik Is An Image Annotation And Machine Learning Software, To Digitally Isolate The Vasculature From 3D Images Of Islets Previously Generated By Ms. Creasey. The Machine Learning Algorithm Classifies Certain Voxels Of The Image As Borders Of Certain Features Of The Islet. So, As I Annotate The Edge Of Blood Vessels, The Program Will Hopefully See Other Edges Of Blood Vessels And Notice That They Are Similar To The Edges That I Am Annotating, Subsequently Filling In The Gaps.
- Imaris
- Once The Annotations Are Completed, I Will Quantitatively Analyze The Segmented Results Of The Structure Of The Vascular Network Inside Each Islet Using Imaris. Imaris Turns The Output From Ilastik Into A 3D Object That I Can Virtually Manipulate. Using This 3D Object, Different Metrics Will Be Measured.
The workflow goes from raw data -> FIJI + Ilastik -> Imaris -> measured metrics. That’s all folks! Thank you for reading and the answer to the riddle is below :).
Memory