Grid Problem

I am a PhD student in Tissue Engineering at the University of Twente in the Netherlands. I am an user of the CellProfiler.

I have a few querries regarding the S/W. I’ll be grateful if you could suggest something to overcome them.

I am working on a Chip containing 40000 wells and the cells are confined within these wells. The wells are in the shape of a square. I’ll be grateful if could answer the following questions.

Can you please suggest how I can quantify data from each individual wells.

Right now I’m laying the grid but the cells in each of my grid unit are counted as one unit. I’d want to have details of individual cells in each grid unit.

Many thanks in advance. I look forward to hearing from you.



Hi Hemant,

Assuming that your chip has well-defined wells of regular spacing and size, it sounds like you may want to make use of DefineGrid in order to define the individual compartments. From there, you can then make measurements on a well-by-well basis. Take a look at the yeast patch images under the Examples directory (or you can pick up the relevant files at …


Some more ideas for you: it sounds from your original post that you’ve been able to identify each well of your grid as its own object (and if not, Mark’s DefineGrid/IdentifyObjectsInGrid suggestion should help). If you have indeed successfully identified each well of the grid as a separate object, then you will next want to use an IdentifyPrimAutomatic module to identify each individual cell (irrespective of which well in the grid the cells live in). Lastly, use the Relate module to associate each individual cell (‘child’) to a well (‘parent’). That will allow you to measure the properties of each individual cell but associate each cell to a particular sample in your array.
Does this help?