DR. HANNEMAN'S MINERAL COLLECTION WILL BE AVAILABLE FOR SALE IN THE NEAR FUTURE
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 Post subject: New Microscope & Image Stacking
PostPosted: Sat Nov 07, 2009 3:37 am 
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Well the deal was too good so I bought it! I got a new microscope with camera adapters and it's pretty nice. I ended up with an Olympus SZH10 with both dark-field and normal base illumination. It also had the camera adapter for a c-mount video camera, and after a little working with some more adapters and misc odds'n'ends I managed to get my Nikon D300 working with the system.

I purchased Helicon Focus for increasing depth of field a couple of months ago and wanted to use it with the new system. I shot several images but was not happy with the test results. I decide the problem was controlling the overlap factor between images. For those who don't know about Helicon Focus it works by taking a series of images each with a slightly different focus point on the sample. The software then picks the sharp part of each photo and applies them to a single image. The result is vastly increased depth of field.

I needed to control the positioning of the sample at even increments with good control down to small fractions of an inch. I decided to built a gadget to accomplish this. I got a milling attachment from Taig Tools. It is a micro adjuster connected to a small vise mechanism. http://www.taigtools.com/c1220.html

I attached the base of the unit to a piece of flat polycarbonate and made a small polycarbonate shelf for the vise to hold. When the knob is rotated the shelf can be moved in a controlled fashion. The adjustment control is calibrated in thousandths of an inch. A photograph of the gadget is shown below with a small mineral sample of vanadinite.

Image

The gadget is placed under the lens of the microscope and focus is first achieved at the highest point on the sample using the focus knob on the scope. A photograph is taken, the knob on the gadget is then adjusted to raise the sample a fixed amount. In the example below I used 5/1000 of inch for each increment. I ended up shooting about 50 images as the sample moved through all of the focus planes. Here is the unit positioned under the scope.

Image

This first image shows the first photograph recorded before the set of images were enhanced with Helicon Focus. Notice the top edge of one crystal is in focus the remainder of the image is well out of focus. The width of the entire image is 10 mm.

Image

The next image was created using the stack of photos in Helicon Focus. It is very apparent that the image now shows good focus throughout the range. The gadget works well in controlling the sample's rise through the various focal planes.

Image

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PostPosted: Sat Nov 07, 2009 3:42 am 
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very smart!


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PostPosted: Sat Nov 07, 2009 7:04 am 
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That is sweet..very innovative and well done!

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 Post subject: Pseudo-Animation
PostPosted: Sat Nov 07, 2009 12:31 pm 
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For any who want to see it in pseudo-working condition here is an animation I have been working on - will use it for a class I am teaching next year in Macro/Micro photography ...

http://www.theimage.com/apubimages/micromovie.mov

(Needs quicktime to view)

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 Post subject: Some more trials
PostPosted: Sat Nov 07, 2009 6:59 pm 
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Here are four stone with large inclusions, I wanted to try out the image stacking as the inclusions were either deep or at different levels within the stone. (I'm going to have to work more on lighting now as it's hard to get directional light into such small areas.) I also notice that the positioning is more critical as any veils that appear between the scope and inclusion are now going to be sharp and block the item(s) being photographed. Normally you can focus through somethings and they just slightly blur the image, but now they can obscure it.

Image

Example 1 is some pyrites in a small quartz cut stone. They are distributed at three different levels within the stone.
Image

In this stone there is evidence of some pyrite crystals having been weather away. If the pryrite located along a fracture or can come in contact with the quartx surface then it can be destroyed by the action of air and water.
Image

Here is an interesting graphite crystal which was cut so that it runs diagonally down into the stone.
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Finally a graphite inclusion that is nearly as large as the table of the stone, and is actually very deep into the cut quartz. The stone itself is about 5mm on a side. The table is 3mm across.
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Last edited by theimage1 on Mon Nov 09, 2009 11:49 pm, edited 1 time in total.

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PostPosted: Sat Nov 07, 2009 7:39 pm 
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Whoa, so this is what you've been up to. :lol:

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PostPosted: Sun Nov 08, 2009 7:35 am 
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Hi Ron,

i found you solution VERY smart and your picture are for sure VEEERY cool, congrats!!! :D
now i was thinking... why you would move the stone up and down and not focusing it by the pod instead?
i usually shot inclusions picture at high mag factor, almost never big specimens so maybe this soultion couldn't be suitable for me.. :roll:
then there's the problem to have the inclusion with the same illumination, for example under the darkfield.... if i move the stone up and down the light will be totally different and it's improbable i could have a decent image by stacking pics, no?
just some free tohughts...
ciao
alberto

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PostPosted: Sun Nov 08, 2009 8:39 am 
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Great images!!
I too had in mind the same questions as Alberto.

Also, kudos to mr Krebs for that piece of software, I know he is considered one of the top photomicrographers around with several awarded images.

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PostPosted: Sun Nov 08, 2009 10:25 am 
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it would be nice to find a solution for who, like me owns a stereomicroscope with the camera fitted on the photoport (or ocular).
when you are shooting pics at high mag with this setup and you focusing on the object you'll see even a very little "sliding" of the subject. so if you stack some pictures of the same inclusion you'll likely have some trouble due to this sliding.... :?
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PostPosted: Sun Nov 08, 2009 12:51 pm 
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I hadn't even thought about the lighting situation changing this way... indeed, that would mess things up completely...


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PostPosted: Sun Nov 08, 2009 11:01 pm 
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That's nice! Will try this technic ASAP.
Congratulation, nice work!


Olivier


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 Post subject: Moving the sample
PostPosted: Mon Nov 09, 2009 12:16 am 
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As far as the fulcrum and vibration is concerned, I agree. But I have some dampeners built into the system and I don't currently believe it is having a major effect on me. The effect can be mitigated by moving the sample further toward the support. Or maybe to be more precise, I think I have far more practice to do, and problems to over come than that particular one at this time.

As far as moving verses stationary light ... You got me ... sort of.
I have proved to myself it doesn't matter.

Lets look at the fist diagram below and not be concerned for a minute about the position of the lights. We first need to agree that moving the object on the platform up toward the main objective lens is no different than moving the microscope(B) down toward the object(A). When we use the large or fine focus knob we are actually moving the entire scope body(B) up or down the base-connecting pole. We are adjusting a worm gear(C) that makes the actual travel happen. Hence only an observer looking from the outside would know if the sample got moved or the scope got moved.

Image

The only change in the system in the distance between the main capture ocular in the bottom of the scope and the subject matter (object A).

Now lets consider three different lighting scenarios:
Case 1.) light coming straight down from the axis of the viewing lens. (Some scopes actually offer an attachment that provide light through the viewing lens system.) Mine does not have this feature, but if the demo scope in the diagram did, then the lighting would not change whether the scope or the sample moved. The light being connected to the viewing axis and the direction of motion only provides a mechanism for the intensity of the reflection to change. Light falls off by 1/R2 (R squared).

Now this is true for any position of the lights you choose. Even if we keep the distance between the original light and the sample(A) fixed, the other distance (the reflected light) changes by the 1/R2 rule as that distance will change regardless of which moved.

As far as moving the light source with the sample, I did do this initially, not so much to control the various light angles, but because I wanted to use a ring light on the scope and it would typically sit around the main objective housing. So if any of you are currently using this set up then moving then focusing the microscope for multiple image taking will have the same "changing the light" effect as moving the sample.

The idea of using a ring light is to provide even 360 degree illumination and negate this effect. The light is also located as near to the center of focus as possible like the interior lens-light described above, again mitigating the effect. The little gadget I first made is pictured below. I wanted to keep the light as close to the object (sample) as possible to get maximum illumination. I used a plastic cylinder on the moving base and put the sample into the center of it The light was clamped on the outside of the cylinder and the whole unit moved up and down with the slide. Thus the lighting was effectively constant without regard to position. See next photos ...

Image

I discovered that this introduced a new problem which is related to the lighting set-up I will describe below. The light being located near the sample top or an equatorial position on "some" samples produced internal shadow or (more accurately) added diffusion in the sample and provided poor viewing. This was the case in some gemstones where the internal flaw (item of interest) was surrounded by a veil or tiny bubbles.

Case 2.) Assume the light is at nearly a right angle to the object being photographed. If there is only one light source from one side or the other, then a strong shadow is produced on the opposite side. Think of this as the "sun-rise" or "sun-set" scenario. A small change in position of the object, will cast a much wider or shallower shadow with relatively little movement up or down. Thus during morning or night, in the "big" real world shadows are elongated to a high degree and seem to grow or shrink rapidly as the sun sets or rises. I submit in most microscopy photographs we try NOT to use this set up. We supply multiple light sources to open shadow areas. The only time the effect might be warranted is if we need to accentuate a very fine pattern in a sample. For example really fine etch lines is a crystal surface.

If you are trying to light a more or less clear gemstone to highlight an internal feature this lighting can backfire if the feature is within a cloud of other features. If the other features are solid, then they cast little shadows on the object of interest, or if they are translucent they will scatter the light making focus very poor.

Case 3.) light from above but not concentric with the focal axis. In most of my work I use multiple light sources to surround the object being photographed. This is done not just to reduce shadows but also to get sufficient light on the image for reasonable photography. Microscopes "eat light" in their precision and fine optics. Just like the low depth of field problem in a scope, the light passing through multiple layers of even "fine optics" continues to diffuse and remove light.

One thing which helps remove shadows and limit specular highlights is to use diffuse light. This works against the "intensity/strengthening" effect of light, but diffuse light really helps eliminate strong specular reflections where all information is lost. If you look at the second part of the first diagram there is a poor but roughly accurate light path map for a light being reflected from a crystal located below. (Yes it's an over simplified image, there are actually an infinite number of cones rising up from all positions in the sample ... that's just too hard to draw!)

Reflect light never comes from a true point source, and unless the reflected surface is nearly a perfect mirror, it diffuses the reflection itself. The reflected light from a typical light source (even a halogen fiber optic) produces cones of reflection and they spread-out as they travel away from the object. Only those outer most parts of each cone that actually strike the object lens (C1 and C2 in diagram) can be bent back and used to construct the image. Any falling outside the objective lens continue passing on to oblivion as far as the image is concerned. When we change the distance between the objective and the object being photographed we change the "field of view" of the final image. Hence some cones exit in the lower C1 position that will miss entirely in the higher C2 position.

SImple test, put a mm scale under the scope in place of the sample. Set the focus on the scope then adjust the magnification so that the outside edges to two mm markers just appear touching the edge of the field of view. Now move the fine focus knob two full revolutions in either direction. The two markers that were on the edge of the field of view will now be inside or outside the field. This means that items in the original field have either grown or shrunk slightly. Hence light angles hitting portions of them have change in the image.

Or ... look at the first and last photo in a deep stack of images, the outside edge cannot line up as the one taken from one end of focus are not present in the other. The good news for most of us is that much of the software we use will reposition the images in the stack or provide a means for us to do it.

From my (and I admit) limited experience thus far in stacking, if the lighting for the microscope is diffuse and relatively even, this will easily negate the changes in direction from stationary light source and the moving sample. (Basically one of the prime ideas in using a ring light.) Hence after doing about a couple dozen sets of images I have mostly stopped using the moving ring light, I see no major advantage. The only problem I do see is that when I poorly light a subject the specular reflections tend to be slightly larger than they should be. They appear to migrate slightly and broaden.

I personally believe we often spend a way too much time worrying about the "perfect system", there is no such thing. Everything we do to enhance one thing will always negatively effect another. Physics provides us with the saying ... there is no free lunch! Find a system that works for you and turn out results. I think it great to read about what others are doing as it aids us in our own learning and helps us see things in a different way. I enjoy seeing the gadgets and gizmos other use to solve problems.
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PostPosted: Mon Nov 09, 2009 12:21 am 
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Alberto -

I have not played with darkfield illumination yet, so am not certain if it is a good or bad solution. You just sort of made me even think about it. The lighting paths would be truly tortured. :twisted:

This is the first time I ever owned a microscope that had darkfield built-in.

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PostPosted: Mon Nov 09, 2009 4:12 am 
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Wow Ron, thank you for the explanation, you raised some very interesting points!

i would add a bit here but this can be assumed valid for taking pitures of inclusions only. You know, we use many different lights and sources to have a proper illuminating and effective shot. sometimes i usually start from the darkfield only and then, if necessary add some extrernal sources as, for example fibers at different angles to create the desired effect/reflections. This may be the case of an included colored crystal. if i use the darkfield only i can hardly have the color of the crystal coming out, so usually i add a "touch" of direct light (filtered or not, it depends..) , just to illuminate the crystal. Sometimes the whole setting up operation needs a lot of time to be adjusted in the desired way. There are even some cases for which i had to give up after almost an hour of struggling... :? So, at this point you have all fixed to shot the picture AND... ALL the illuminating setup is not connected with the pod, so, by tilting the pod only i can easily shot multiple pictures and stacking them without moving the illumination pattern. Let me say that this would be impossible to do with your solution... :roll:
but i'm always open to everyone suggestions to improve my technique... :wink:

theimage wrote:
This is the first time I ever owned a microscope that had darkfield built-in.


could you post a picture of your darkfield setup? Just curious..

ciao
alberto

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PostPosted: Mon Nov 09, 2009 11:37 am 
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Ron, when working with faceted stones and tiny inclusions the slightest movement of light gives a whole different image so for inclusion photography it may not be the best set-up. That said, for minerals etc it will do the job perfectly...

Alternative: buy a wild M400 and you have super fine focus built in your scope :D


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