the-vat

Class project for adam2392 and ttomita

https://github.com/Upward-Spiral-Science/data/tree/master/syn-diversity

Contact

Handle: adam2392

Email:ali39@jhu.edu

We are working on synapse diversity within the brain with image data gathered from array tomography.

ToC

Assignment 1

./Draft/summary.md

Significance and Feasability analysis of my proposed project topic

Assignment 2

./draft/questions.md

Asking the 6 types of scientific questions about my project topic

Assignment 3

./code/descriptive_and_exploratory_answers.ipynb ./Code/Exploratory_analysis_tyler.ipynb

Begin answering my descriptive and exploratory questions. Once I've answered them I will go back and revise the questions I asked - discuss those I couldn't fully answer, ask follow up questions that would be informative, etc.

./draft/UpdatedToDo.md

Updated the questions based on our initial analysis - After Midterm presentation

Assignment 4

./code/inferential_simulation.ipynb *./Code/inference_tyler.ipynb

Formally asked inferential question about my data, and answered it on simulated data from the null model, alternate model, and real data

Assignment 5

./code/classification_simulation.ipynb

Formally asked classification question about my data, and answered it on simulated data from the alternate model, and real data

Assignment 6

./code/test_assumptions.ipynb ./Code/assumption_checking_tyler.ipynb

In the previous two assignments, we made assumptions about our data. Now, we will check them and see whether or not they are true, and if not, update our understanding or assumptions about our data to those which are more right.

Assignment 7

./draft/summary_presentation.pdf

Presentation about findings and methods used throughout the project.

Assignment 8

./docs/progress_report.md

Report stating all analysis completed to date, as well as logical next steps.

Assignment 9

[./code/extended_exploratory.ipynb](./Code/newexploring/exploratory analysis.ipynb) ./Code/exploratory_analysis2_tyler.ipynb

10 more questions and plots about my data. Shows a suite of BIC plots for transformed data and filtered data by synap values at 25, 50 and 75%. Did separately for f0, f1, f2, and f3 instead of all together.

Assignment 10

[./code/multiple_distributions.ipynb](./Code/newexploring/clustering analysis.ipynb)

Testing the clustering with a k of 4, 5, 6 on f0