I am trying to set up an automated way of measuring the apical area of drosophila pupal wing cells. An example of the type of picture I’d start with is shown below
The subapical adherens junctions between the cells are labelled with ECadherin-GFP. As you can see it is a very simple tissue with the two primary cell types (vein and ‘intervein’) easily distinguishable by apical cell area.
I tried to modify the ‘Tissue neighbours’ example pipeline but came up with 2 issues:
- The 'overlay outlines' module would often put in junctions where no junction existed (i.e. through the middle of a cell). An example of mislabelled junctions is shown below:
As a result, many more cells were identified than were there, and average apical area was much smaller than it should have been.Is there a way of manually removing false junctions? Or is it just a case of changing the thresholding method?
- Ideally I’d like a table of stats for the area of each individual cell measured in the picture, not just a summary of average cell area and standard deviation. Is there anyway of getting this?
I’m probably missing something obvious, but any tips would be very helpful.