I have found that the best way to get the GAIN "right" in MOSFLM is to
have a look at the optimum "Sdfac" parameter at the end of SCALA (the
first of the three SDCORRection values). Specifically, if SDFac is > 1,
then you need to increase the GAIN. This is because SDFac>1 means that
the spots were noisier than MOSFLM thought they should be, and if a
given number of ADU is noisier than expected, then there must have been
fewer photons involved in generating the signal. This means that the
"true gain" was higher. Yes, there are other sources of error, like
shutter jitter, beam flicker, calibration errors, absorption effects,
scale factor errors, etc. But these are all directly proportional to
the intensity, and therefore accounted for by adjusting SDadd (the last
of the three SDCORR values). SDfac accounts for noise proportional to
the square root of intensity, and only shot noise (like photon counting)
behaves like that.
David Waterman makes an excellent point that the point-spread function
(PSF) acts like a smoothing filter and makes the background look less
noisy than photon-counting error permits. This makes the
BGRATIO-estimated GAIN lower than the "true" GAIN. However, one can
argue that this is not always a bad thing, since the error in measuring
the intensity of a given area of flat background really is "better than
photon counting". This is because you have the smoothing effect of the
PSF working "for you": bringing in signal from areas outside the region
you are measuring (prior knowledge of "flatness" if you will). However,
this smoothing effect of the PSF does not apply to spots because spot
photons all arrive in essentially the same place, and no "smoothing"
will change the intrinsic noise of the total number of photons that
actually arrived. The upshot of this is that we really need two
different values for GAIN, one for the background and one for the
background-subtracted spot intensity. The influence on sigma(I) would
depend on the relative contributions from the spot vs the background
under it. I am pretty sure this is not implemented.
It is perhaps interesting that there is also a third type of noise which
is independent of the spot intensity: "read-out noise". This used to be
called "fog" on film detectors. Despite all the money we spend on
detectors that minimize it, there is no specific accounting for read-out
noise in MOSFLM or any other integration package I am aware of.
However, a "trick" to account for it is to simply lower the ADCOFFSET.
For example, using 1 A X-rays on an ADSC Q315r detector in hwbin mode,
the true GAIN is 1.8 ADU/photon, the ADCOFFSET is 40 ADU, and the
read-out noise is equivalent to the noise deposited by ~2 photon/pixel
of x-ray background. This means that a blank image has an average value
of 40 ADU and rms variation of ~2.5 ADU, but this is equivalent to an
image from a detector with the same gain, no read-out noise, and
ADCOFFSET of 36 that was "fogged" by 2 photons/pixel (regardless of
exposure time). Yes, this is a small change in ADCOFFSET, and I doubt
you will notice the difference. I think this speaks to the fact that,
on modern detectors at least, read-out noise is essentially negligible.
Another way to get the GAIN, of course, is to measure it directly. I
did this on an ADSC Q315 detector in swbin mode by comparison to a
NaI:Tl scintillator (after accounting for the window and sensor
thickness of the latter device):
http://bl831.als.lbl.gov/~jamesh/pickup/Q315_gain.png
You can see how the GAIN changes appreciably with photon energy, and
this is largely because lower-energy photons generate less signal. GAIN
also changes with the detector read-out mode. For example, this number
is 3 times higher for a Q315r in hwbin mode. I have listed my best
information on the typical GAIN and read-out noise of common detectors
on my "minimum crystal size" page here:
http://bl831.als.lbl.gov/xtalsize.html
You can extract the parameters by selecting the "detector type = " you
want, and then switching it again to "Custom..."
-James Holton
MAD Scientist
On 3/3/2011 12:34 PM, Bryan Lepore wrote:
wondering if mosflm can automatically estimate the gain.
i.e. i gather it is still estimated the usual way.
-Bryan
