BioApps are typical imaging workflows in the field of Life Science Research and similar or related fields. Typical steps involved are
- Image Acquisition with certain parameters on specific imaging systems
- Image Processing and Analysis
- Data Processing
- Visualization of the results
Typical example for such applications are:
- Cell Counting
- Scratch Assay
- Translocation Assay
- Live vs. Death Assay
- Proliferation Essay
- Confluence Measurements
- ...
This repository will contain some useful Image Analysis Settings, tools and scripts that can be used for various things "surrounding" those BioApps.
The Image Analysis Settings (*.czias) can be used inside ZEN Blue or ZEN Core with the example images. Depending on the real images those settings must be obviously modified.
Since the concept of Open Application Development (OAD) is about connecting the ZEN world with other valuable software tools, those example will also contain non-ZEN scripts etc.
Those two short videos demonstrate how to do a simple cell count in ZEN blue and display a heatmap. The 1st video explains how to setup the IA analysis and the 2nd video shows how is runs in Real Time (on a laptop).
Remark: The heatmap is shown at the end of the 2nd video.
Image Data:
- CZI file with 96 scenes from a typical wellplate sample carrier on a CellDiscoverer 7
- file size is rather small = approx. 1GB
The image analysis is quite straight forward and included the following steps:
- Smoothing using Median Filter
- Triangle Threshold
- Filter small particles
- Fill Holes
- Separate by Watershed