CellProfiler Adjust Brightness/Contrast to mimic FIJI ImageJ

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cellprofiler
imagej

#1

Dear Community,

A quick question here -

Could someone suggest the best way to mimic the following FIJI ImageJ command directly within CellProfiler -

Image > Adjust > Brightness/Contrast > Auto > Apply

Many thanks,
E


#2

Good day Emma,

as you can see from the ImageJ User Guide SubSection 28.2.1:
Every click of “Auto” increases the image contrast with 0.35% over-exposed pixels.

The essential question however is, for what reason or purpose do you like to see this operation.

Regards

Herbie


#3

Hi Herbie,

Thanks for this.

Effectively, I’m doing this to aid visualisation of images for manual outlining of objects. (Raw images appear very dark with no variation between pixels by eye, but histograms show there is a real change in intensity between pixels.)

Ideally, I’m looking for a setting in FIJI ImageJ that will best spread my pixel values across the full 16-bit range (without over-exposing if possible). Any suggestions on this count greatly appreciated!

In terms of replicating in CellProfiler - I am looking where possible to include as many operations as possible in a CellProfiler pipeline rather than moving between FIJI ImageJ, CellProfiler and other softwares.

Any advice you can give would be much appreciated.

Many thanks
E


#4

Emma,

in order to help, I’d need a typical raw sample image as 16bit TIF. However I can’t help with CellProfiler.

I’d recommend a histogram evaluation and the according setting of an upper and lower threshold. This can be done by avoiding any clipping of the image data.

Regards

Herbie