What am I doing wrong?

Just bought that first macro lens? Post here to get helpful feedback and answers to any questions you might have.

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rjlittlefield
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Re: Update

Post by rjlittlefield »

ChrisLilley wrote:
Sally wrote:Anyway, I think I'm getting somewhere - I have bits in focus:
http://www.sallyswebsite.com/SAL_0677.jpg

This is a 100% crop of the bits in focus.
Sally
That is looking a lot better, to me.
This looks good. Looking at the 100% that you have posted, at another 500%, I can clearly see focused detail at the level of individual pixels. Examples are at x=275,y=113 and x=354,y=115.

Stack this up at 0.01 mm spacing and it should look good.

--Rik

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Post by NikonUser »

If we are discussing the 10x Nikon Apo , NA 0.45 then 0.01mm is too coarse.
You are going to need at least 0.005mm and possibly finer.
NU.
student of entomology
Quote – Holmes on ‘Entomology’
” I suppose you are an entomologist ? “
” Not quite so ambitious as that, sir. I should like to put my eyes on the individual entitled to that name.
No man can be truly called an entomologist,
sir; the subject is too vast for any single human intelligence to grasp.”
Oliver Wendell Holmes, Sr
The Poet at the Breakfast Table.

Nikon camera, lenses and objectives
Olympus microscope and objectives

rjlittlefield
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Post by rjlittlefield »

Hhmm... To clarify...

http://www.microscopyu.com/tutorials/ja ... index.html shows the DOF of this objective as being about 0.005 mm (5 microns).

At 0.01 mm some of the finest details will definitely get lost in the gaps, but I speculate you'll still be pretty happy with what's left.

However I don't have one of these lenses to test with so I don't know for sure.

NU, do you have any samples showing what sort of degradation might be expected with a focus step of 0.01 mm? For example do bristles or fine hairs start breaking up into "beads"?

--Rik

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Post by ChrisR »

Edit - on rereading I realise this wouldn't have made too much sense at first, it's a bit convoluted.

I have an APO lens like yours, and a D700.
It shows just sharper than the Nikon 10x CFN NA 0.3 160/0.17 which is loved by many forum members. There are tests here which show that a little better than the Olympus 20mm f2.0, which is reckoned to be a bit above the Photar.
So it goes, from best down.
your Apo 10x
Nikon 10x NA 0.3
Olympus 20mm
Photar 25mm

I found the APO better than the NA 0.3, but not a lot. That could have been because the pixels are quite big in the D700, so it can't resolve all that the best lens might provide. This comes from the diffraction effects:
Running the numbers at
http://www.cambridgeincolour.com/tutori ... graphy.htm
You'll see you're somewhere about the cusp of seeing any improvement, because of the large pixels in the D700.

To cover the full 35mm field, you'll probably want to increase the sensor to objective distance. That will increase the magnification, to perhaps 15x.
That may give theoretically degraded performance, but if not, would make the otherwise unresolved detail match the pixels better.

I don't have a Photar, but the extra WD would be very desirable, and I imagine it would cover the field a lot better than a scope objective. At least you do have the option of stopping down to do fewer than the couple of hundred pics you'd need for a typical stack!
I understand what you're saying of about actual single image sharpness, but I think the depth of field is so small that you won't get much of anything sharp if it's not flattened by a coverslip.

Sorry I can't run a quick test, I don't even know where it is. Too much life in the way at the moment!
Last edited by ChrisR on Thu Jul 22, 2010 11:57 am, edited 2 times in total.

ChrisLilley
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Post by ChrisLilley »

rjlittlefield wrote:Hhmm... To clarify...
http://www.microscopyu.com/tutorials/ja ... index.html shows the DOF of this objective as being about 0.005 mm (5 microns).
I guess the DOF depends on the assumed circle of confusion, and also the wavelength chosen.
ChrisLilley wrote: Using your D700 pixel pitch to get a circle of confusion of 30 μm, and seeing that you are using your D700 on a PB-4 which has a maximum extension of 180mm, the total maximum sensor to objective distance is 46.5mm+180mm = 226.5mm. (More if you are using a spacer ring between the D700 and the PB-4).

With a 10x 0.45NA objective, at a sensor to objective flange distance of 150mm (160mm tube length - 10mm eyepiece offset) i.e 103.5mm extension on the bellows, yields an optical magnification of the rated 10x, an effective aperture of f/12.2 and a depth of field of only 9.4 μm.
Re-running that calculation, I assume that the smallest circle of confusion is one which can resolve two points, which is three photosites. (The actual CoC may be larger, due to the antialiasing filter, but that represents a lower bound on the CoC).

The D700 has a large pixel pitch of 8.45 μm, which gives a CoC of 3* 8.45 = 25.35 μm.

For a dry objective (refractive index = 1, for air) I understand the DOF to be

DOF = (λ/NA^2) + c(1/(m.NA))

where c is the circle of confusion, NA is the numerical aperture, λ is the wavelength and m is the magnification. I understand that λ = 550nm is typically chosen as representative for green (red and blue wavelengths will give somewhat different results) so plugging all that in gives a DOF of 8.4 μm.

This is still larger than the 5 μm you quoted; where do our assumptions or formulae differ?

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Post by rjlittlefield »

ChrisLilley wrote:where do our assumptions or formulae differ?
Short answer: It's in the CoC.

Long answer: It's in the CoC. The relationship between CoC and DOF is not nearly as simple as it's usually presented. Let's look deeper...

Assume a circular aperture, a perfect lens, and ignore diffraction. Then when the lens is defocused, any single point on the subject turns into a uniformly illuminated circle of light on the sensor. Conversely, every point on the sensor is illuminated by a circle of points on the subject. As a result, the image becomes blurred.

A good way to think about the blur is in terms of the Modulation Transfer Function (MTF) of the defocused lens. As with many MTFs, the MTF of a defocused lens starts near 1.0 for low spatial frequencies (coarse detail), drops to exactly zero at some high spatial frequency (fine detail), then goes negative for even higher frequencies, and oscillates with decreasing amplitude beyond that.

Here is a picture and a graph illustrating how this works for a defocused lens.

Image Image

On the left we have a sine curve of intensity, as seen through circular apertures of varying sizes. On the right, we have a graph of Modulation Transfer Function as it depends on the circle diameter. Looking on the left, you can easily see that with the largest circle, equal in width to 1.5 line pairs, there is more light than dark within the circle even though the circle is centered on a dark bar. This causes contrast reversal. With the smallest circle, contrast remains high, and with the medium circle, contrast is low though still positive. Looking more closely on the right, you can see that
  • For a small circle, the MTF approaches 1.
  • MTF drops to 0.5 (50%) for a circle whose diameter is about 0.71 of a line pair.
  • MTF drops to 0 for a circle whose diameter is about 1.22 line pairs.

We need also to touch on sampling. The Nyquist sampling theorem says that you need at least two pixels per line pair. But in practice (and in more accurate theory), you need more like three pixels per line pair to reliably give usable contrast. For purposes of discussion, let's assume three.

Now, let's go back to the numbers that you used.

As I understand your calculation, you essentially ended up using a CoC that is three pixels wide. That's 1.0 line pair, which gives an MTF of 18% -- contrast reduction of 5.5X -- for a spatial frequency that is well resolved by the sensor. At the Nyquist limit of 2 pixels per line pair, that same CoC is 1.5 line pair, which is beyond cutoff and will exhibit contrast reversal.

So, a smaller CoC is required.

Exactly how small is sort of a judgment call. If we want to retain 90% MTF from defocusing, at a frequency of three pixels per line pair, then we need a CoC of more like 0.87 pixel. Using the D700's pixel size of 8.45 μm, this gives a CoC of 7.35 μm. If we're willing to retain only 50% MTF from defocus, then we can get along with a larger CoC, more like 18 μm.

Of course I started off by saying "ignoring diffraction". It turns out that accurately determining the combined effect of diffraction and defocus is far from easy. Some months ago I snapped a copy of an article that treats it in quite a bit of detail, but I have yet to spend enough time to really digest it. (I think that would take several days.) However, I suspect that the numbers we just computed are not too far out of line.

We are fortunate that the formula you're using is the same one that Nikon uses at http://www.microscopyu.com/tutorials/ja ... index.html . Plugging 18 μm into that page gives a DOF of 6.7 μm; plugging in 7 gives 4.3.

So where did my "5" come from? Danged if I know -- I think I just cranked the Nikon calculator down to something around 10 μm which I've found to give results that kinda sorta match what I see in practice.

But I will happily admit that this is a very imprecise process, and no way did I run through the calculations that I just now wrote up for the sake of discussion. In fact the illustration and graph that I've posted above are freshly generated from scratch, since at the moment I'm quite far from my usual resources. I think they're correct, but I'm not sure.

I hope this helps. If anything looks wrong be sure to let me know because I hate messing up the literature.

--Rik

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Post by rjlittlefield »

I forgot to mention, there is an example of contrast reversal at http://www.microscopyu.com/articles/opt ... intro.html. See Figure 8 and surrounding discussion.

--Rik

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Post by ChrisLilley »

Rik, thanks for this; reading it now. I notice that you treat 'line pair' as one black, one white line; while I was thinking of the minimum separation of two points (two airy disks) to resolve them as separate points, hence the 3 pixels (black, white, black).

Sally, sorry if this is more detail than you were expecting from an apparently simple question.

The reason it matters (besides a desire to really understand how things work) is that many common linear stages have a 10 μm minimum shift. Whether the DOF and usable step size is close to or far from 10 μm is thus of direct practical interest. Also, like you, I like my apochromatic photography lenses and would have initially thought to get apochromatic objectives as well. I may well do, in the future, once I am sure that I will have the equipment to use them.

Sally
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Update

Post by Sally »

I've now removed the cover glass from the objective - I couldn't tape it on completely flatly, and was getting distorted corners. I haven't noticed a drop in quality since taking it off - which leads me to believe that my initial inability to get a sharp picture was a combination of the wrong tube length and stray light rather than a lack of cover glass.
Thank you to all those who spent time with the technical info - I must admit, a fair bit of it was over my head - but in time I'm hoping I'll understand more of it.
My next challenge is getting my lighting right.

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