I am working on a collaboration with Mia Cellavie where we are trying to figure out the best way to measure the PSF of a microscope from a collection of beads. We want to measure and collect 3D statistics for all beads in the image, and output them in a table.
We also have been looking into potentially using KNIME for this task, as it would make it easier to analyze many images, with multiple channels.
I’ve been having trouble getting some KNIME nodes to work on 3D images. And it looks to me that a specialized work flow is needed for 3D measurements. For example the thresholding and connected components nodes seem to only process the first slice of an image. Or am I missing something?
Should I just look to ImageJ2 and
ops for 3D processing? I was thinking I could modify the Ops_Threshold_Measure into a command, then integrate it with KNIME. Or is there an easy way to do it in the current KNIME?
Anyway for the next couple of days we are going to be brain storming approaches to this project. We anticipate being able to share work that gets developed. If anyone has any suggestions on any tools we should look at, please let me know.