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Nikon D7000 read noise, gain and thermal noise

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#1 sharkmelley

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Posted 19 February 2013 - 06:04 PM

Apologies for the length of my first post but I hope you find it worthwhile.

I have been doing DSLR astrophotography for a few years mainly using an old modified Canon 350D. However I recently heard that on the D7000 model, Nikon have updated the infamous "Star Eater" Hot Pixel Suppression algorithm for long exposures which used to remove not only single hot pixels but clumps of up to 4 adjacent pixels i.e. stars. It now only removes isolated hot pixels in long exposures.
If you want to know more, see this post on DPReview:
http://forums.dprevi...s/post/37071846

However, it's been almost impossible to find any firm data on its suitability for astrophotography, so with the help of a friend who owns one, I decided to put it through its technical paces.

Taking pairs of frames at different shutter speeds of a diffuse white object allows the gain and read noise to be calculated. Then taking 24 dark frames of 5 minutes each allows the dark current and hence thermal noise to be investigated.

My results are summarised here:

Posted Image

The figures in bold are figures I have calculated (most of the analysis was done at ISO 800) and the rest were inferred by assuming the gain doubles for each halving of ISO.
I find it odd that the gain for the Red and Blue channels is different from the Green channel. But my figures are confirmed by examining the histograms of pixel values in the raw NEF files. The Green channel has every integer pixel value represented in the histogram but there are gaps in histograms for Red and Blue. The frequency of the gaps (14 gaps / 100 values) agrees with the ratio of gains of the Green and R/B channels which is approx 1.14

Posted Image

Unfortunately this is not the only pre-processing of data that Nikon performs before writing raw (NEF format) images. The 5 minute dark frames had well over 50% of pixels with zero value - it seems to vary between 50% and 80% zero valued pixels from raw darks I have seen from different examples of the D7000. Does this mean that the dark current is ultra-low? Unfortunately not. It means that the values have had a constant value subtracted from them, clipped at zero, to make the thermal noise appear less intrusive. If you plot the pixel values from a dark frame as a histogram you should normally see the familiar "bell-shaped" normal distribution curve. But all that remains in the D7000 dark frames is the high end tail of this distribution - more on this later. However by taking the difference between pairs of successive frames and then trying to fit the tail to a complete distribution (lots of maths!) I was able to approximate how the dark current (and hence thermal noise) increases over the 2 hours taken to perform 24 exposures of 5 minutes each - a typical astro-imaging scenario.

Posted Image

For interest, compare this with a number of Canon cameras I have tested:

Posted Image

So there are 2 pieces of really good news:

1) The read noise of this camera is more or less constant at an extraordinarily low level for all ISO values. At ISO 200 you have a gain of almost unity (very useful because electrons only appear in whole numbers!) with incredibly low read noise. If you are shooting raw frames (which all astro-imagers ought to be doing) there is no reason at all to use higher ISOs - you would get no improvement in overall image quality and your images would saturate more quickly (i.e. the dynamic range reduces). I would actually argue that there should be no obvious difference in quality if you do all your imaging at ISO 100 on the D7000.

2) The dark current is also very low indeed. Notice that these measurements were taken at an ambient tmeperature of 20C. For every drop of 6-7C, the dark current will reduce by a factor of 2 and the thermal noise will reduce by a factor of 1.4 (square root of 2) On a cold night (typical in the UK!) this camera is capable of producing long exposure images with extraordinary low noise levels with huge dynamic range. Shooting in normal daylight daylight conditions, exposures will be short and thermal noise is not measurable.

But there are 3 pieces of bad news - all related to the way that Nikon pre-processes the data before writing the raw NEF file.

1) The HPS algorithm, although improved, can still mean that using short focal length lenses, a star occupying a single pixel will be erased. However, with many sub-exposures stacked together this is unlikely to be a big issue.

2) The Red and Blue channels are scaled by 1.14 (why?!) leading to the gaps in the histogram. This is only a slight annoyance to the purist like me and probably has no visible effect.

3) The bigger problem is the clipping of pixels to zero. If you use this camera at slow F-ratios, on a warmish night in a very dark place you will see pixels with zero value. Data in dark shadowy areas (e.g. dust lanes of nebulae) is being thrown away and you'll never be able to recover it by stacking how ever many images you stack. Why does Nikon decide to throw your your precious data away? In practice, this may or may not be a problem - it really depends on the scope/lens you are using and the conditions you are shooting under. But it is certainly likely to affect results from narrowband filters (e.g. H-alpha). I would be really interested to hear experiences from anyone who may have already encountered this.
But the bigger problem associated with pixel clipping is that it is actually impossible to shoot proper calibration frames i.e. dark frames and bias frames. Both darks and biases will contain at least 50% zero value pixels. You might go through the motions of taking many dark frames and summing into a single "master" dark but that master dark is not correct, the values have been distorted by the clipped pixels. They won't do a proper job of removing thermal effects from your image. The same with bias frames - they will not do a proper job of removing "pattern noise". However it is difficult to quantify what effect this has on the final stacked image. Also I am trying to think of a way of "biasing" dark frames and vias frames with very low levels of light to push all the pixel values up to the level where no clipping takes place.

So, in conclusion, the sensor (Sony Exmor IMX071) in this camera is an extraordinary sensor with extremely low levels of read noise and low levels of thermal noise - especially on cold nights. It is a real shame that the issue of clipped pixels exists but then again some imagers will never notice this nor the effects it has on their images. You never know, maybe some day a firmware "hack" will come along that enable this to be switched off.

Clear skies!

Mark

#2 ccs_hello

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Posted 19 February 2013 - 10:43 PM

Hi Mark! Welcome to Cloudy Nights!

Thanks for your thorough analysis on D7000 and brought up Marianne Oelund's thread on DPR. Her study was not so well known here in CN (I only read her's last week on my IMX071 study <-- long story I'll describe more in later days.) But I highly recommend CNer's to go there reading it. Basically it's about N's modification on its infamous "Star Eater" (need mode 3 to help) feature, i.e., Hot-Pixel Suppression (HPS) algorithm. Then N "enhanced" it (the new 8-neighbor algorithm) P.S., it's been going for a while and a few feel its acceptable and mode 3 is no longer needed. Luckily it kind of align with N's change from CCD based to CMOS based DSLRs.

Let's exchange some notes:

Back to black level clipping, My gut feeling is that many mfgs are doing the same. Prof. Craig Stark's paper showed that on C's.
Many Review sites are using DCRAW based raw file decoding, while the camera mfg. alter the actual OBP (Optically Black Pixel) values and change these to a mfg supplied fix value to make the picture "clean". There is a new RAW decoding library (looking my note now) which can defeat that and let the user select the black level for proper sensor characterization.

Going back to D7000, my study on IMX071 is that Pentax K-5 and K-01, Sony NEX-5N, and others seem to track the identical sensor performance curve (using DXOmark) so may be it's not the body doing the black clip (and is not just N by itself) but the sensor itself. But at this point, it's just my guessing.

Now the IMX071 itself. Now we know its internal PGA (programmable gain amplifier) is no longer doing extra gain any more after ISO1600. Anything beyond is just digital scaling (left shift, multiply by two)! (Pentax at this stage run software enhancement, appears to look like one extra stop gain).

Anyway, I am getting a cam using IMX071. I'll know more.

Please keep us apprised with great info!

Clear Skies!

ccs_hello

#3 guyroch

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Posted 19 February 2013 - 11:01 PM

That's a good informative *first* post. Welcome to CN.

I have a feeling your contribution will create some good conversation. :bow:

Guylain

#4 ccs_hello

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Posted 19 February 2013 - 11:07 PM

Mark,


RE:
2) The Red and Blue channels are scaled by 1.14
N' being N is its rather rigid way of treating itself as a leading edge mfg. in imaging space. Sticking to precision is its job - to sell cameras (while scaling may ruin the perfect scientific use of image sensor :), i.e., allowing us to use post-processing.) Oh, the reason... recalibrate to compensate the not so perfect Bayer filter spectrum response to fit the ideal color gamut.
BTW, N's HPS is famous, isn't it.

RE:
3) The bigger problem is the clipping of pixels to zero.
Let me dig out the reference of using the RAW decoding (replacing DCRAW) that can ignore "manipulated" OBP value and see how it goes.

Clear Skies!

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#5 Astronewb

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Posted 19 February 2013 - 11:25 PM

Thanks so much for the interesting read. I image with a Nikon D5100 (same sensor), so I found it very interesting. My 'sweet spot' may be dropped from 400 to 250 or 320 now.

Great read...cheers

Paul

#6 ccs_hello

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Posted 19 February 2013 - 11:48 PM

About D7000 and D5100 ISO selection...

Indeed for max dynamic range, use low ISO (100 or 200), then the burden will be mount tracking, etc.

Since the sensor used has a very low noise, for shorter exposure time in imaging, I'd say up to ISO 1600 with reduced D.R. Beyond that there is absolute no gain since it's just digital scaling (while chop more bit off D.R.)

For low light LiveView/observ type of useage, go ahead use max. ISo possible. Per DXOmark's performance curve, at 25600 you still get 6 stop D.R. and reasonable S/N which IMHO is still very usable.

Clear Skies!

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#7 cherokawa

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Posted 20 February 2013 - 12:30 AM

About D7000 and D5100 ISO selection...

Indeed for max dynamic range, use low ISO (100 or 200), then the burden will be mount tracking, etc.

Since the sensor used has a very low noise, for shorter exposure time in imaging, I'd say up to ISO 1600 with reduced D.R. Beyond that there is absolute no gain since it's just digital scaling (while chop more bit off D.R.)


Please bear with me - I'm a newbie at this. But doesn't unity gain at ISO 200 mean that at any ISO beyond this there is only digital padding? In other words, 5 mins at ISO 200 will have the same SNR as 5 mins at ISO 1600 - just that the ISO 200 image will be dimmer and this can always be stretched in post-proc? Just trying to get my understanding straight. :help:

And Mark, thanks for a fantastic and informative post. :)

#8 orlyandico

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Posted 20 February 2013 - 06:54 AM

http://www.sensorgen...NikonD7000.html

read noise is about 3 e- and the well depth is 50K e- at ISO 100.

at ISO 200 the well depth is 19000 e- (as expected).

QE is 48%

some other cameras -

http://www.sensorgen.info/

(model / QE / read noise / well depth)
EOS_5D 25% 4.2 55297
EOS_5D_MkII 33% 3.2 64600
EOS_5D_MkIII 49% 2.4 67531

none of these cameras come close to the 80% QE of the early-2000's Kodak ST-3200ME. Any reason for that? or is the above QE simply due to the Bayer sensor? or due to the small pixels? the 5D Mk I has large pixels (8um) but miserable QE (25%)

Seems that the D5200 has the best numbers on the above web site..

#9 ccs_hello

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Posted 20 February 2013 - 07:51 AM

Re: (Does)(if) unity gain at ISO 200 mean that at any ISO beyond this there is only digital padding?

Not the case, the PGA does the amplification until there is (1) no significant benefit (yes, the noise part starts to degrade S/N, but only to the extent that "gain" helps in fishing out the signals) to amplify it further more
(2) noise starts to be a dominate term (too high a gain on PGA) such that digitally scale would become a better straegy

For IMX071, the cross-over point is around ISO1250 or so.

Again, my point: use low ISO for more dynamic range and better quality astrophotography. Can go a bit higher if you want to use that apparatus to help you to "see" (frame and focus) or get image quicker (e.g., mount limitation etc.) If you can tolerate more degradation, use even higher ISO (i.e., in-camera higher than ISO1600 or use post-processing techniques)

Clear Skies!

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#10 sharkmelley

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Posted 20 February 2013 - 07:58 AM

About D7000 and D5100 ISO selection...

Since the sensor used has a very low noise, for shorter exposure time in imaging, I'd say up to ISO 1600 with reduced D.R. Beyond that there is absolute no gain since it's just digital scaling (while chop more bit off D.R.)


Please bear with me - I'm a newbie at this. But doesn't unity gain at ISO 200 mean that at any ISO beyond this there is only digital padding? In other words, 5 mins at ISO 200 will have the same SNR as 5 mins at ISO 1600 - just that the ISO 200 image will be dimmer and this can always be stretched in post-proc? Just trying to get my understanding straight. :help:


I may be wrong about this but I have a strong suspicion that the raw digital data from the chip is simply multiplied by different constants for each ISO. The Exmor sensor has a ADC unit for every column of detectors. If I'm right, nearly every ISO should have the same SNR but of course the dynamic range will change. So higher ISOs would gain you nothing at all.

#11 ccs_hello

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Posted 20 February 2013 - 07:58 AM

DXOmark or sensorgen's figures reflect image system's figure of merit. It may have other components tinted by the camera mfgs.

Kodak's reflect the sensor itself. Note that the KAF-3200 is a monochrome and full-frame type CCD, not interline type of CCD nor CMOS APS image sensors.

I would caution that Q/E is simply a parameter in the sensor's figure of merit (pay attention to noise figure and dynamic range, pixel pitch, etc.)

Clear Skies!

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#12 Magellan

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Posted 20 February 2013 - 10:04 AM

Wow what I post! great job!!

I have been looking for one of these for a 450D, do you have one by chance?

#13 srosenfraz

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Posted 20 February 2013 - 11:21 AM

Mark - welcome aboard and your first post sure is informative. Glad to have you join the crowd!

@Jeff - Best article I've seen is Craig Stark's article on CN where he analyzes much about the 450D. I think it'll have a lot of the information for which you're looking.

#14 sharkmelley

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Posted 20 February 2013 - 04:26 PM

Back to black level clipping, My gut feeling is that many mfgs are doing the same. Prof. Craig Stark's paper showed that on C's.


That's not my experience of Canons and I've analysed them in quite a lot of detail. They have a fixed bias e.g. 512, 1024, 2048 which does cause it's own problems but not nearly so bad as Nikon's clipping to zero. Do you have a reference for Craig Stark's paper?

There is a new RAW decoding library (looking my note now) which can defeat that and let the user select the black level for proper sensor characterization.


Sounds interesting.

Going back to D7000, my study on IMX071 is that Pentax K-5 and K-01, Sony NEX-5N, and others seem to track the identical sensor performance curve (using DXOmark) so may be it's not the body doing the black clip (and is not just N by itself) but the sensor itself. But at this point, it's just my guessing.


If we could obtain some long exposure dark frames from these cameras we would know for certain. The thing about this clipping to zero is that it is only noticeable on long exposures with no light (or very little light) reaching the sensor.

Now the IMX071 itself. Now we know its internal PGA (programmable gain amplifier) is no longer doing extra gain any more after ISO1600. Anything beyond is just digital scaling (left shift, multiply by two)!


Marianne Oelund indicates this happens after ISO 950:
http://forums.dprevi.../thread/2947801
I think I was wrong with my guess about the on-chip ADC being 16bit - there is some analogue amplification taking place on the sensor. However I still think there is no advantage to using ISOs higer than ISO 200 which gives more or less a gain of unity. Once you are counting individual electrons there is nothing to be gained by trying to count half electrons or quarter electrons!

Anyway, I am getting a cam using IMX071. I'll know more.


Me as well! My analysis was done on a friend's camera. One of the first tasks will be to mod it for H-alpha - I'm dying to know its H-alpha sensitivity.

Mark

#15 ccs_hello

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Posted 20 February 2013 - 09:58 PM

Mark,

Craig's paper in his website here which is a little bit revised. RE: the OBP swap out, you have to read the paper careful to derive your own conclusion.

RE: IMX071AQ family used in
D7000, D5100, K5, K-01, A580, NEX-5N, (perhaps NEX-C3), etc.
Indeed we need astro specific characteristics, especially on long exposure based low photon flux related testing.

(Or baby IMX071, the IMX109AQE used in
Panny GH3, E-PL3, E-PM2 and Oly OMD E-M5
They are fantastic too.

RE: the sensor on-chip column-parallel A/D Converters (few thousand of them) used in SONY Exmor sensor.
They are 12 bit only.

Clear Skies!

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#16 sharkmelley

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Posted 21 February 2013 - 02:50 AM

Craig's paper in his website here which is a little bit revised. RE: the OBP swap out, you have to read the paper careful to derive your own conclusion.



Yes, I'm familiar with that paper. Although the Canons do shift the histogram (by a variable amount) the paper is not saying it results in the "clipping to zero" problem that the D7000 shows.

RE: the sensor on-chip column-parallel A/D Converters (few thousand of them) used in SONY EXMOR sensor
They are 12 bit only.


But the ADCs on the D7000 sensor are 14bit right? I'm now convinced that it is not a 16bit sensor.

Mark

#17 harbinjer

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Posted 21 February 2013 - 11:35 AM

I'm pretty sure that the K-01 and the K-30 don't use the same sensor are the K-5. It is similar in many ways, but it definitely has a lower dynamic range.

#18 Astronewb

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Posted 21 February 2013 - 01:49 PM

One of the first tasks will be to mod it for H-alpha - I'm dying to know its H-alpha sensitivity

Here's an image of IC's 405 and 410 taken with a modded D5100, 5 minutes subs @ISO 400. They have pretty good dynamic range and low noise, now I want to try it at ISO 250!

Posted Image
IC405/IC410 Crop by Astronewb2011, on Flickr

Cheers,

Paul

#19 ccs_hello

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Posted 21 February 2013 - 08:18 PM

Yep, discussing DSLR performance is tricky and sometimes heated in many forums. Study on DSLR body is not the sensor itself. (And RAW is not sensor raw!!!) One has to read in between the lines to make sense of it. Unfortunately, it is subject to interpretation.
Anyway, K-01 and K30 use the same sensor, K-5 is tiny, tiny bit improved, but I think it is using software techniques in the body.
K-5's ISO 80, 25600, and 51200 are in "extended" mode, which means (using your imagination,) software techniques.

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#20 ccs_hello

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Posted 21 February 2013 - 08:23 PM

Mark,

RE: "Canons do shift the histogram (by variable amount)"
Isn't that the drop the low values first?


About the sensor dynamic range, Nikon follows its D300 tradition (in low-ISO, does a slow speed image acquisition with 14-bit resolution, while using a 12-bit sensor IMX021.) I think this time, it's going to be the same mystery, squeeze IMX071's 12-bit column-parallel ADC to become an effective 14-bit image acquisition.

My gut feeling is either N is using a software technique, post-sensor; or there is really using a (possible) undocumented IMX071 readout mode (non-destructive pixel readout) ( <-- I am guessing here, no solid proof its APS structure has the circuit do that) such that the same pixel got read twice (or more times) to estimate more sensor bits.

Clear Skies!

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#21 sharkmelley

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Posted 22 February 2013 - 03:18 AM

Mark,

RE: "Canons do shift the histogram (by variable amount)"
Isn't that the drop the low values first?


No.

Suppose in an example long exposure the thermal noise has a mean of 400 electrons. It will then have a standard deviation of 20 electrons - the square root of 400 (this relationship is a property of the Poisson process of photon arrivals). This means over 99% of the pixel values are within 3 standard deviations of 400 i.e. 99% are in the range 340-460. This electron count is then scaled by the gain and shifted so it's mean is the usual bias for that camera, say 512. It's extremly unlikely for any pixel to end up with a zero value. I don't think I've ever seen a Canon long exposure dark frame with pixels clipped to zero.

By contrast, the Nikon deliberately shifts the distribution to the point where at least 50% of the pixels are clipped to zero. But in typical cases, 80-85% pixels are zero-clipped.

My guess is that Nikon is using the electron counts in the "optical black" border of the sensor to determine the amount to subtract from all the pixels on the chip. The trouble is, the optical black border is the warmest area of the chip from my experiments, so it is has thermal electron counts higher than the rest of the sensor. So if the subtraction level is set so the average level of the pixels in the optical black border, it will be severely destructive to the pixel counts in the rest of the sensor and this is exactly what I am seeing, 80-85% zero-valued pixels in a dark frame.

It's not only darks that are affected. I can think of many real world astro-imaging situations where the D7000 will start pixel-clipping. Now, if you are taking single images or stacking a few frames together the effects may not be noticeable. Unfortunately, once you start stacking 100 sub-exposures of 5minutes together (which I do all the time for a typical image) then these effects will become very obvious.

I've now found this article online where the author(s) describe(s) exactly the same problem with the Nikon D300:
http://theory.uchica...D300_40D_tests/

Their statement on the D300 agrees with my conclusion on the D7000:

"The nonlinear distortion of deep shadows in [Nikon] D300 raw data by clipping means that it will be a poor choice for astrophotography, or any application where pulling weak signals out of the noise at very low illumination levels is of importance."

In fact, the more I think about this the more I become doubtful about purchasing this camera. As far as I can see, this is probably the best sensor out there at the moment on a budget DSLR and I really want to like it. It has the capability of producing fantastic noise-free astro-images. But then the pre-processing of the data by the D7000 compromises it.

Mark

#22 sharkmelley

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Posted 22 February 2013 - 12:04 PM

Here's a image that may be of interest. I've taken average statistics from the final 20 dark frames of 5 minutes - from the 2 hour session for estimating dark current. In the image below, the brightness corresponds to the percentage of non-zero pixels.

Posted Image

I've annotated areas where 90%, 80% and 70% of the pixels were clipped to zero. In the corners only 40% were zero.

So this image also gives an indication of where the sensor is warmer i.e. the corners and sides.

Mark

#23 Hemlock

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Posted 22 February 2013 - 04:14 PM

Great post - if anyone's interested in further testing darks, I'm pretty bored over here in Cloudchester!
At my disposal
- D7000
- D5100
- D300
- D600
(sorry, wish I had the 5200)

#24 sharkmelley

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Posted 22 February 2013 - 08:32 PM

Thanks Hemlock.

The D5100 has the same sensor as the D7000 so I would be interested to see if it behaves the same as the D7000 and if the heat build up is similar. It would need 12-14 darks of 5 minutes at room temperature - each immediately following each other. Raws of course!

Mark

#25 Hemlock

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Posted 23 February 2013 - 03:16 PM

I'll work on this today, you were testing at ISO200, right?






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