I am new to Knime. I have turned to Knime because I want to reduce variability between experiments by choosing the best threshold for each experiment. Testing multiple thresholds for 7 samples in 5 experiments is time consuming in Cellprofiler and I am hoping to automate testing thresholds in Knime.
Looking at the “speckles” example workflow, I think what I want to do is create a new node before the “Execute pipeline” node that lists multiple thresholds to test. As I said, I am new to Knime. Is this how you would go about it @christian.dietz ? Has anyone already made a similar workflow in Knime? I think it would be generally useful. I have colleagues who count spots by hand instead of using automated image analysis because of the problem/time-consuming process of selecting a threshold for each experiment.
For some more background on my setup: I have a Cellprofiler pipeline that detects nuclei, red spots and green spots. It then assigns each spot to a nucleus and counts the number per nucleus. Finally, it measures the number of overlapping spots per nucleus.