Project:  Exploring Anatomy with Images

Prologue: Gudmap allows the visualization of gene expression on specific GU anatomy. This knowledge is imperative for the understanding of pertinent diseases and ensuing treatments. Improve existing interface and improve it.  The goal of the project is to improve the annotation of histology images. A histology image is typically stained with two specific stains namely hematoxylin and eosin. Each image shows the genito-urinary the tissue regions or tracts of either humans or mice (murine). It should be also noted that each image is essentially a stack of images at various scales and magnifications. Further the images could additionally have In-situ gene expression maps where certain specific genes are probed for expression.

Resources: Please find

1. Class slides here.

2. The existing tool can be found here.

3. Prof. Kirk McHugh, Department of Anatomy, OSU will serve as the expert.

4. The rationale for the GUDMAP tool can be found in these papers: manuscriptA, manuscriptB, manuscriptC.

5. Do not think of this project and data as solely belonging to those who do biologists. It is really spatial data exploration.

6. Please find a comprehensive user study on GUDMAP conducted by a professional outfit on Piazza. Please do not circulate. Use this as an example.

7. Another similar respository and set of tools can be found here. These tools explore gene expression in developing brains (of mice and men).

The Data:

 Please visit – TBP.

Deliverables: The project should have all these components.

1. Complete a user study as we discussed in laboratory assignment 4. Create a list of tasks, and have some peers examine the list.

2. Next do one of two things

a. Create a mockup (no coding) and complete a second user study as a focus group and demonstrate that there was an improvement. You will need to at least use 5 or more views of data.

b. Or, using at least two views, create a new tool that incorporates the first user study. No second user study is needed to show improvement.

c. The tool should

i. annotate regions of tissues on a single and multiple scales.

ii. Overlay the gene expression on the images.

d. When you complete the user study and evaluation, please do not use the “example user study” verbatim. The user study addresses the layout of the web site rather than the process of annotating, marking, and detailing

3. Write a report.