How do you apply data science to your projects?

'We operate a wet lab and a microscopy lab that generate loads of data. Especially image data can be big as it is multidimensional (a.o. x,y,z,time,color). So we need to use data science approaches to process and visualize these data in a swift, reproducible and standardized way.'

Is there a project from this past year that you are most proud of? 

'I received a Grassroots grant and I used it to generate a dashboard that collects and displays data from students that participate in a practical course. The students measure the size of human cells with a microscope and upload the data. Currently, the dashboard has >2000 entries from 3 years and each year (when the course runs) new data will be added: https://amsterdamstudygroup.shinyapps.io/CellSizeR/'

What do you like most about being a DSC member?

'It’s fantastic to be able to meet people from entirely different disciplines (who I normally would not meet) that have a similar interest. Additionally, the workshops that are organized by DSC have been super useful. It is a great network to be part of to learn and also share experience or knowledge.'

What is your favourite data science method?

'I’m really into data visualizations, and I’m collecting different types that we’ve made. To enable others to make similar plots (in R with ggplot2) I have published “protocols” that explain in step-by-step fashion how to recreate these: https://joachimgoedhart.github.io/DataViz-protocols'

Are you camp Python/R/or something else?

'Ouch, tough one. I’m experienced with R and only learned to properly use Python a year ago. I love R for data Visualization, but it’s hard to beat Python for Bioimage Analysis.'

Contact Joachim Goedhart about his work