I have a set of images coming from a single microarray scan of cells, and different images correspond to different wells on one glass slide. I am trying to get some statistics of each cells’ close neighbours using the following settings:
However, when we looked at the analyzed data, in Well #1 (=Image #1), the number of neighbours are all 1. In Well #8, the number of neighbours are all 2 (with a single exception). This was extremely unreasonable. Especially for #8, it is almost impossible to have such a perfectly even distribution in an unpatterned well. Moreover, while there is no intrinsic differences between the wells, the neighbour counts on other wells do vary from 2 to 200.
Hence we took a more careful look at the data, and found further evidence that something goes wrong (at least in well #1):
From the 3 highlighted lines, we could derive the following information:
Cell #1, whose closest neighbour is 24.5 pixels away, is considered to have 1 neighbour within the defined range (I think the range is 15+15=30 pixels, as both identified objects would be expanded equally)
However, Cell #8, which is 24.5 pixels from Cell #1 and 5.8 pixels from Cell #11, is also considered to have 1 neighbour within the range.
Is that actually a bug? Or am I misunderstanding something?
I have also attached the images, the pipeline, and a copy of the output excel sheet. The software version is 2.1.1. Thanks very much.
Input Images and Pipeline.rar (1.94 MB)