I have very big variation of staining between the dataset and I would like to know if my workflow is correct.
I’m not sure about the step 4…
I already did some trial with machine learning (thank to @haesleinhuepf @Pete and @Research_Associate for the help) but the researcher ask me to analysis the data with a more basic methods.
Duplicate image and I detect the tissu with gaussian filter and Huang threshold
Image calculator to calculate only collagen or nuclei in tissu
I calculate the mean intensity of the collagen in the tissu and I apply different threshold based on the value. if mean of means < x I apply Otsu threshold , else Li .
to do that I use analyze particles in the tissue and I multi-measure mean in the collagen image. Then I create an Array and I use Array.getStatistics(array, min, max, mean, stdDev) to extract the mean of the means
Please find the mean of the means of collagen staining in the tissu (not the entire image) slide 1 to 23
- I continue with the measure of the area etc etc…
Can I split my dataset like this because the staining have been made by different people and at different moment (+/- 10 month between the first and the last). And it results of different intensities of staining.
This not look very ethical but if I don’t do that I will overestimate collagen in some slice and underestimate in other slice