I am using: CompiledCellProfilerXP325811Bugfix, working on Windows XP 32
I’m trying to count segmented objects over multiple planes. Each object may show up in multiple planes, but I only want to count it once.
My upstream pipeline PIPELINE#1 generates product images called “GrayObjects”. I have developed a pipeline to stack the gray segmented images into a single image and then to resegment this final image at the end.
I have attached a pipeline PIPELINE#2 that works well for a set of 8 images. I can refer specifically to the GrayObjects images 1-8. That would be OK if I wanted to do only one set at a time. But if I want to use the upstream pipeline (that created the output files) to analyze multiple stacks of 8 I get into trouble. For example, if I analyze 4 stacks, I will have 32 output GrayObjects images, numbered 1-32. that doesn’t work in this pipeline.
I can think of a couple of approaches:
If I run the two pipelines in series using the “Run Multiple Pipelines” command, it runs all 32 images in PIPELINE#1 and then switches over to PIPELINE#2. I wouldn’t have the problem if it switched back and forth between PIPELINE#1 and PIPELINE#2 for each set of 8. There must be a way to do this, but I don’t know it.
My Stack_Tracking pipeline is cumbersome Stack_tracking_PIPE_8_planes.mat. It requires me to load the 8 files in two steps, because I can only load 4 specific files at a time, and then to name specific images for each step. If instead of working with specific files (GrayObjects 1-8) I were able to add the images as a group of 8 and ratchet down the list for each subsequent step of the imagemath module. I have done this with MetaExpress, using 0, +1, +2 to tell it to compare the current plane (0) to the next plane in the stack (+1), etc. Does this make sense?
a. Is there any way to do this in CellProfiler?
b. How could I do it in groups of 8 and start a new group when I reach the 9th in the series.