BioVisVisualization in Biology

What is BioVis

Biological Data Visualization helps researchers in life sciences to gain insight from their data by extracting different features out of their data as well as helping them asking the right questions and guide them to the right conclusions.

BioVis Fields

Microscopy Next generation Sequencing

Visualization and Data Analysis in Molekular Biology

● Data Analysis in Next Generation Sequencing● Usability of existing tools● Workflow optimization and customizability● Usable Image Segmentation and Classification● Visualization of statistical features in cell cultures

Existing tools

● Complicated to use● Specialized for own needs● No maintenance● Ressource hungry and high runtime● No documentation --> Provenance Problem

Testing for viable technologies

● Database Approache● Python vs. Rust● Usability Focus● Testing existing tools

Why don’t you use “better” tools?

Lessons learned?

Why does Visualization in Molecular Biology matter?

“It doesn’t”

Lessons Learned

•Tools are not maintained or stable•Bioinformaticians is not a Standard•Misunderstanding of what Visualization is•Developing with Usability in Mind•Containers to avoid environment issues•Not only “one purpose” tools

•Data Provenance Problem in molecular biology “All downstream analysis was performed using custom R (v3.3.2) and bash scripts” – Nature 2018

BioOptics

● Image Segmentation for Cells/Nuclei● Cell Tracking● Classification and finding Regions of Interest● Find interactive Visualizations for Statistical Features in

Cells

Ilastik

Cellcognition Explorer

Visual Data Exploration in BioVisResearchers often don't know how to quantify or measure findings

Outlook: Automated Microscopy

● Let the microscope do all the work● Only help it in defining Regions of Interest● Provide Visualizations for the statistical Features of Cells