Object measurments

Hi;
could you please specify how the objectIntensity is calculated. I’m trying to measure cell flourescence and the measurments I get from cellprofiler are vary different then the ones I get from other programs.

thanks;
michal.

Hi Michal,

Do you mean that the values are within the range of 0 and 1? If so, this is CellProfiler’s default behavior; images are rescaled so that the maximum value is 1 by dividing the all pixels by the aximum possible intensity value.

If you mean something else, let us know.

Regards,
-Mark

Hi Mark,

there are values betweenn 0 and 1, but there are also higher values in the integratedIntensity section. what do thoes mean?
also, is the intensity calculated fot the whole object or just at the x,y location? and what’s the differense between meanIntensity and edgIntensity?

thanks,
Michal

Hi Michal,

Integrated intensity is the sum of the pixel intensities in the object. So depending on the size of the object and the intensities involved, the sum can easily be greater than 1.

The pixel intensities are calculated for each object for MeasureObjectIntensity.

MeanIntensity is the average pixel intensity within the object, whereas EdgeIntensity is the intensity along the object edge.

For future reference, these details are included in the module help. The help for each module describes the measurements that the module makes and you can access it by selecting the module in your pipeline and clicking the ‘?’ button below the pipeline panel.

Regards,
-Mark

Hi again,

Is there a way to get the object measurments in the original units not rescaled to 0 - 1 ?

thanks,
Michal

Not with the currently released version, but our developer version has a checkbox which will allow you to disable rescaling. For more details on this, please see this forum thread in which the user has a similar issue. Please note the caveats on the trunk build page referred to in the final post.

Regards,
-Mark