Yes, I made sure to include a color chart standard in every picture for color white/black balance and color correction! Sadly, lighting couldn't be controlled for due to these being colonies in situ at differing depths and taken on days where the natural lighting varied, meaning that there will be no way to perfectly standardize all the pictures even with the standard. However, we have a good number of photos which should help account for some of the noise that this creates.
-Andre -----Original Message----- From: John Cahill <[email protected]> Sent: Wednesday, February 28, 2024 2:05 PM To: [email protected] Subject: Re: Histogram help Note: This message originated from outside the FIU Faculty/Staff email system. Adding to Michael's comment about illumination I would suggest you include a standard in every imaging session. By imaging and measuring each time you will have better confidence in the results. On Wed, Feb 28, 2024 at 4:50 AM Michael Schmid <[email protected]> wrote: > Hi Andre, > > for color images, the "standard" histogram display depends on the > setting of Edit>Options>Conversions>Weighted RGB Conversions. > > If this option is on, the intensity on the x axis of the histogram > plot is calculated as 0.299*R + 0.587*G + 0.114*B and labelled > "Intensity (weighted)". > If "Weighted RGB Conversions" is off, the intensity is calculated as > (R > + G + B)/3, and labelled "Intensity (unweighted)". > > In "R+G+B" mode, the histogram shown is the sum of the histogram of > the histograms of the individual channels, i.e., the value for > intensity 0 is the sum of the number of pixels where R=0 plus the > number of pixels with G=0, plus the number of pixels with B=0. You > will also see that the number 'N' of intensity values examined is > three times as much as the number of pixels. > > If you want to examine bleaching, you are probably interested in color > saturation, so you could convert the image to a HSB stack and look at > the saturation and its histogram. > > There are also nice plugins for color inspection, e.g. the 3D Color > Inspector/Color Histogram by Kai Uwe Barthel > https://imagej.net/ij/plugins/color-inspector.html > > Of course, you have to make sure that illumination conditions and > white balance of the camera are always the same. Accurate color > measurements are a science on its own... > > Michael > ________________________________________________________________ > On 27.02.24 19:53, Andre Briscoe wrote: > > Hello, > > > > I am currently working on designing a method to use ImageJ to > > estimate > bleaching in corals using the histogram function and was wondering > what is being represented in the R+G+B graph in case it is the graph > best suited for what I am trying to do. Does anyone happen to know? > > > > Best, > > Andre Briscoe > > PhD Student > > NSF CREST Center for Aquatic Chemistry and Environment Institute of > > Environment, an FIU Preeminent Program > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
