How to use Illumination correction file from Perkin Elmer Operetta microscope outside of Harmony (in imagej or cellprofiler instead)

Hello,
I am trying to figure out how to use the calculated flat field correction (illumination correction) that a operetta microscope produces in my own cellprofiler pipeline. I was hoping there was a way to possibly build a illumination correction ‘image’ in imagej/Fiji that I could then use in cellprofiler for correction my images.
I believe the file is giving me all the information I need to produce an image that looks like:
http://nic.ucsf.edu/blog/wp-content/uploads/2014/04/FITC_10x.png (not my image)
An example of an operetta FFC_Profile.xml (flat field correction) file looks like this:

<Results xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.perkinelmer.com/PEHH/HarmonyV5">
<Version>2</Version>
<ProfilesComplete>1</ProfilesComplete>
<AggregatedQuality Scope="Background">1</AggregatedQuality>
<AggregatedQuality Scope="Foreground">1</AggregatedQuality>
<Quality ChannelID="1" Scope="Background">1</Quality>
<Quality ChannelID="1" Scope="Foreground">1</Quality>
<Count ChannelID="1" Scope="Background">128</Count>
<Count ChannelID="1" Scope="Foreground">285</Count>
<Map>
<Entry ChannelID="1">
<FlatfieldProfile>
{Background: {Character: NonFlat, Mean: 3747.8228, NoiseConst: 4.0573891, NonFlatness: {Corrected: 0.049106896, Original: 0.44735402, Random: 0.027165147}, Profile: {Coefficients: [[1.1523], [0.0635, 0.0631], [-0.9058, 0.0382, -0.7466], [0.002, -0.1096, -0.0296, -0.253], [-0.3628, -0.1935, 0.2453, -0.0644, -0.9442]], Dims: [2160, 2160], Origin: [1079.5, 1079.5], Scale: [0.00046296296, 0.00046296296], Type: Polynomial}, Quality: 1.0}, Channel: 1, ChannelName: "*Alexa 647", Foreground: {Character: NonFlat, NonFlatness: {Original: 0.48933411, Random: 0.061149477}, Profile: {Coefficients: [[1.1134], [0.0265, -0.017], [-0.4092, 0.0168, -0.5735], [0.1694, -0.2256, 0.4858, 0.0598], [-0.9208, 0.2278, -1.8684, -0.3317, -0.5632]], Dims: [2160, 2160], Origin: [1079.5, 1079.5], Scale: [0.00046296296, 0.00046296296], Type: Polynomial}, Quality: 1.0}, Version: Acapella:2013}
</FlatfieldProfile>
</Entry>

Thank you.

1 Like

I hope I understood your question correctly. For ImageJ, this might be useful:
https://imagejdocu.list.lu/howto/working/how_to_correct_background_illumination_in_brightfield_microscopy

Once you produce the right image (like the PNG you point to), it’s trivial to apply it in a CellProfiler pipeline using CorrectIlluminationApply.

However, the way Perkin Elmer is storing the information in that file is pretty funky. If no one is aware of a converter from PE format to an actual image, I’d suggest contacting PE support to ask them. I wonder if the software itself allows exporting as an image?