MFI: mean, or median, fluorescence intensity?

Mario Roederer roederer at
Thu Feb 21 06:51:54 EST 2008

I see no reason that MFI must be expressed in SI (W/m²); as far as I  
am concerned, any units are acceptable as long as they are defined.   
By convention (and if undefined), the units on measurements in flow  
cytometry are arbitrary; this does not make them unreasonable as units  
for reporting values.

You must be careful if you use "MFC", though.  In many cases, channel  
numbers are NOT linearly proportional to intensity (for example, on  
analog instruments with log amplifiers, which was virtually all  
measurements prior to a few years ago).  Only on some of the newer  
digital instruments, like Aria and LSR II, are the measurements stored  
in channel numbers that are linearly related to intensity,  
irrespective of the displayed transformation.

Thus, if you compute your measurements as MFC for events collected on,  
say, a FACSCalibur, then what you are actually reporting is the  
geometric mean fluorescence -- a very different statistic (albeit also  
a decent measure of central tendency).

Thus, computing and labeling as MFC is acceptable (as long as you  
define the abbreviation) -- but in doing so must also define whether  
you have channel numbers that are log-scaled (meaning that MFC is  
proportional to geometric mean fluorescence intensity) or linearly- 
scaled (with MFC proportional to MFI).	In my opinion, this  
unnecessarily confuses the issue.


(PS, if you are actually computing the MFI, as most software does,  
then labeling the results as MFC would be incorrect on instruments  
with electronic log amplifiers.)

On Feb 21, 2008, at 12:50 AM, rozenkov at wrote:

> To be even more scientific:
> “In physics, intensity is a measure of the time-averaged energy  
> flux. The word "intensity" here is not synonymous with "strength",  
> "amplitude", or "level", as it sometimes is in colloquial speech” / 
> Wikipedia, Intensity (as much as Wikipedia is scientific)/
> The units of electromagnetic wave, or light intensity in SI are W/m²  
> (watts per square meter). In our case we are talking about channel  
> numbers. They do represent intensity, but the numbers that we see  
> are numbers assigned to channels, hence MFC, not MFI.
> I often see in papers fluorescence “intensity” graphs with the axis  
> labeled MFI, but I always label my graphs MFC, which is what the  
> axis units actually are – channel numbers (whether mean or median).
> Vladislav Rozenkov
> -----Original Message-----
> From: Mario Roederer <roederer at>
> To: Cytometry Mailing List <cytometry at>
> Sent: Tue, 19 Feb 2008 6:22 am
> Subject: Re: MFI: mean, or median, fluorescence intensity?
> Since MFI is not a "generally accepted" abbreviation (for journals),  
> it has to be defined anyway in manuscripts.
> Given that it could refer to either statistic, it should always be  
> defined even in less formal settings (e.g., EMail).  That being  
> said, I would hazard a guess that "mean" is far more commonly-used  
> and most people will assume "mean" if not explicitly defined  
> otherwise.
> To be safe.... always be explicit on the first use.
> mr
> On Feb 15, 2008, at 12:15 PM, Maciej Simm wrote:
>> Dear Group:
>> if I ask google scholar:
>> "MFI median fluorescence intensity"
>> vs
>> "MFI mean fluorescence intensity"
>> I get 3,470 vs 16,100 hits, respectively. So which is it - mean or  
>> median fluorescence intensity?
>> Maciej Simm
>> Tree Star Inc.
>> On Feb 15, 2008, at 5:50 AM, Carl Simard wrote:
>>> [snip] MFI ? [snip]
> =
> More new features than ever. Check out the new AIM(R) Mail!

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