Volker BrunsResearchers at the Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM) have developed PEDRA: Platform for Ex-Vivo Drug Response Assays. Up to 100 compounds are tested in parallel on primary patient-derived cells using High Content Imaging and further methods.
The following video illustrates the image analysis conducted with MIKAIA®.
High Content Image Analysis with MIKAIA®
This video was created with MIKAIA® 2.3.0 and shows the analysis of a single well and subsequent batch-analysis of multiple-wells with MIKAIA®‘s FL Cell Analysis App. Voice-over / speaker: Volker Bruns, Fraunhofer IIS.
Panel & cell type mapping
Each scan shows an individual well from a multi-well plate. The panel includes a tumor marker (EpCAM), an immune cell marker (CD45), and a viability marker. MIKAIA® detects all cells based on the DAPI channel, then measures the mean fluorescence intensity (MFI) per marker and cell. A cell’s type is determined by deciding which markers are expressed and then matching the combination to the configured cell type map.
Inspecting results — Gaining confidence in image analysis
After the analysis has run (ca. 15 seconds for one well), all nuclei are outlined. Cells are assigned to the types specified in the cell type map.
The “cells (by marker)” group contains one annotation class per marker. Cells that express multiple markers yield multiple annotations and, therefore, these annotation classes should be viewed one at a time. They are convenient for inspecting and visualizing which cells express a particular marker.
Conversely, the “cells (by co-expression)” group contains annotation classes per marker combination. Here, each cell is assigned to exactly one of these classes, allowing for simultaneous visualization of all classes.
The video above shows how this analysis is rolled out to a larger dataset. All images are batch-analyzed and results are written to a folder along the way. From the set of output files, the summary CSV file is the most important output file. It contains the desired read-outs per well: cell abundances by type. From this, PEDRA will assess which compound most effectively kills tumor cells while leaving immune cells alive.
Contacts for PEDRA — Platform for Ex-Vivo Drug Response Assays
Lukas Wöhrl
Product Owner &
PhD Candidate
Fraunhofer ITEM
Send email
Dr. Christian Werno
Head of Department of Molecular and Functional Assays
Fraunhofer ITEM
Send email
This project is conducted in the context of
and receives funding by
Fraunhofer Cluster of Excellence
Immune-Mediated Diseases (CIMD)
Anna Chiwona
Add comment