Radial Distribution

Hi there,

I’m using the MeasureObjectRadialDistribution module to analyse mitochondrial distribution in my fluorescent images. My images have multipe cells (2-10), but the output table gives me a single set of figures for each bin. Is the output data an average of the radial distribution of my objects per cell, or is the output only showing me the radial distribution in a single cell?

Best wishes,

Luke

Hi Luke,

The output of MeasureObjectRadialDistribution is on a per-object basis, not an average. Look in your per object table (e.g. “Cells.csv” or whatever the name of the object was that names in MeasureObjectRadialDistribution) at columns beginning with “RadialDistribution_”. If you are referring to the table that displays when the module runs, then yes, for compact display sake, those values are averages across the objects in an image. But as long as you export the object’s data in Export*, then the data is per-object.

Cheers,
David

That’s great, many thanks for the help.

Is there a way of visualising the segmentation that the programme has applied to each image?

Best wishes,

Luke

You can view the segmentation by
(1) Explicitly saving the outlines in the Identify* module (look for “outlines” in the settings)
(2) Add OverlayOutlines module, saving the previously noted outlines onto your choice of image (actually this is optional – if you want you can save just the outlines without a ‘background’ image)
(3) Add SaveImages module to write the new outlined image to disk.

David

Dear David,

Thank you for that, but I think I’ve asked the wrong question. By ‘segmentation’, I meant the segmentation applied during the MeasureRadialDistribution module. Is it possible to generate an output that shows the bins overlayed on the cells in the image? So far, all I’ve managed to do is generate outlines of the primary, secondary and tertiary objects, which I think is where I misled you by talking about ‘segmentation’.

Best wishes,

Luke

Hi Luke,

I see. Unfortunately, no we don’t have a visualization of the radial distribution. I could definitely see the benefit of one, and I will add it to our feature request list.

Thanks,
David

FYI, feature request here: github.com/CellProfiler/CellPro … ssues/1255

Dear David,

Very many thanks for all your help. The discussion and the rough results look great already. I would say however that the heat maps obscure the features of the cell that are being measured by the MeasureObjectRadialDistribution module, and simple thin boundaries for the sections, overlayed on the image would be more helpful in my case.

Best wishes,

Luke

Hi Luke,

I’ve added your boundary pixel request to the Github issue noted above.

Thanks,
David