Vala Sciences

Having some difficulty with simple thresholding and masking in pipeline environment.  I create a simple binary mask via one of standard thresholding techniques.  Debug mode shows this mask is generated.  I then link this mask to a labeled mask, and debug mode shows that this mask is also created.  I can apply the labeled mask to a gray image and this ouput is generated in debug mode.  The problem is that these masks are not deposited into the results folder.  The only mask ouput to the results folder is an archived “labeled mask” in ZIP format.  Can you assist me by suggesting a proper course of action which will generate an image mask that can be used as the basis of pixel metrics?  Thanks for your help, PjB

Self-resolved

Hi Paul,

I’m glad it’s working for now. Sounds like it was quick fix?

Best,

Casey

Hi Casey, ... just a lot of trial and error on order and references of plug-ins. 

We do have a bit of a problem though.  I noticed that the measurment list does not output the Summed (Capital Greek Sigma) mask area in a microtiter well, which also affects total integrated intensity measures.  Can a “measure” plug-in be easily adapted to include this ouput, or, a new plug-in be created for this output?  This is an important measure in the 3D cell cultures of the differentiation assays conducted here in the lab.  It gives us an approximate measure the differentiation efficiency.

Thanks for the help,
PjB

Thanks for creating a new thread created for this question.

Best,

Casey