Dear cell profiler staff,
Congratulations for this nice new release of cell profiler.
I have adapted your example pipe called Neighbours in order to count cells growing in agar. I have 3 cell types, red, blue and green +blue.
Initially I would like to be able to count just blue cells. Everything works except IdentifyObjects, which can not see my cells no matter what treshold method I use. Can you help me to see what’s wrong?
In the future once this is fixed, I would like to measure how many red cells have as a neighbour a green cell and compare with how many has a blue cell, and also orientation if possible (i.e. if there is any self arrangement of cells over time within the microcolony, kind of higher number of individuals (ellipses) whose major axis are parallel). Any suggestion on this will be more than welcome!
Thank you very much in advance for all your help, you are making something really nice in here!
Technical university of Denmark
ExampleNeighbors_adapted.cp (8.87 KB)