MeasureObjectIntensity

Hi!

In the MeasureObjectIntensity module is there a way to chose particular parameters to be measured? In most of the case there is no need to have all of them for analysis. Just thinking if it can reduce calculation time. For instance, I need just ‘Mean Intensity’.

Thank you very much in advance!

Dmitriy

Hi Dmitriy,

No, one cannot pick and choose measurements within a module, though that is a reasonable request. (There are a couple of exceptions to this, e.g. Zernike’s in MeasureObjectSizeShape for just this reason, however in these cases there will be an explicit setting in the module.) We do have a long-standing Github issue on this, but it’s not a high priority at the moment for us. Plus when we do use machine learning on datasets, it is often hard to predict which sets of measurements will be weighted most highly, so we leave them all in.

Note that in ExportToSpreadsheet you can choose what measurements get exported, but that won’t affect the calculation time.

David

Hi David!

Many thanks for very quick reply!

OK, I can live with that!

When exporting data to spreadsheet I use the option to pick particular measurement for exporting and it is very useful. Regarding that I have one more question.

I do “simple” time lapse analysis of fluorescence intensity in cells that can also move a little during recordings, so object tracking is another module we use. However, my question is about measurements representation in spreadsheets: why all the measured values (from all the objects) are in one column (one after another). Is it possible to place data for each object in separate column and use raws for different frames (time point in my case)? With hundreds of objects and thousands of frames it is a problem to manage all the values if they are placed in one column. Could you help with this issue?

Thank you very much in advance!

Dmitriy

I think I understand what you’re asking, but let me know if I’m mistaken. There is no setting in ExportToDatabase to separate out the output in the Per_Object table/csv based on individual objects. The output as-is has the Object_Numbers interleaved:

Image_Number Object_Number Metadata_Frame Measurement1 etc
1 1 0 12
1 2 0 25
2 1 1 5
2 2 1 9

[quote]Is it possible to place data for each object in separate column
[/quote]

There are many measurements for each object (even using a single measurement module, so you cannot place them in a single column (though you could filter all the rest if you only care about a single measurement/feature).

[quote]and use raws for different frames (time point in my case)
[/quote]

Each row is a different frame already, albeit interleaved.

If you want to have the Object_Numbers not interleaved, i.e.
Image_Number Object_Number Metadata_Frame Measurement1 etc
1 1 0 12
2 1 1 5
1 2 0 25
2 2 1 9

you could simply use Excel (or whatever) to sort by Object number, i.e. Data->Sort -> Sort by Column ‘Object_Number’. Better, you could write a little Matlab script to have more control over your data analysis, but that is left to you.

Does that help?
David