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Mineral PhotographyImage Inversion

28th Sep 2015 15:54 UTCRobert Wilken

Hello all,

I have been relatively successful taking micromineral photos for the last four or five years. I had an extra AO binocular microscope and a “state of the art” (maybe 15 years ago) Coolpix 4500 digital camera. It took me many years to get it up and running. It wasn’t until I had an adapter made by Richard Kinch that I was finally able to mate the two components. I found the freeware CombineZP stacking program to do a pretty good job. It was easy to use. This wasn’t world class photography but it was what I could afford and it was at the worst average quality.

Yearning for better drove me into an expenditure of more money about a year ago. I picked up a reasonably priced Ebay Nikon SMZ-T2 trinocular scope. Unfortunately, I made the mistake of buying a boom mount scope which I discovered is much more susceptible to lateral movement/vibration than a table stand. Based on an Imscope Micro Tech review, I purchased a Canon 600 D (Rebel t3i). Anything better than that was way out of my price range. The inexpensive add-ons were a wired remote and an AC adapter so I wouldn’t have to worry about batteries. Between the mirror lock-up capability of the camera, the remote time delay and the fact that the setup is on a basement slab I think vibration (boom problem aside) is pretty well under control.

My results have been horrible with this setup have been horrible.

1. The inverted images are driving me crazy. With my old Coolpix setup I didn’t have the problem; probably because the fixed camera lens was between the sensor and the microscope. But with the Canon, just the camera body is mounted with a t-mount on the photo tube. My reaction has been that I don’t like getting a photo I haven’t composed and planned. Simply rotating the inverted image 180° doesn’t result in the image you really want. I also don’t like the fact that it renders impossible the use of creative lighting e.g. reflected light to highlight crystal facets or striations that would otherwise disappear. My main lighting is dual gooseneck fiber optic. But sometimes I added a second dual unit as well as reflective materials to direct light to otherwise invisible facets. Rarely, even daylight from a southwest facing window came into play. My question for anyone with more expertise than I have is: Would a photo tube ocular setup resolve this issue? And then, if so, does anyone know if an older model Nikon SMZ can accommodate it?

2. My second issue pertains to stacking software. For whatever reason I have found that CombineZP freeware does not seem to be work properly any more…even with fresh downloads. So, I am now in the middle of a Zerene stacker trial. I am coming to dislike it intensely. My observation would be that it may be great for macro photography of insects, shells and flowers but it doesn’t work well for micromineral specimens. The aforementioned nature photography starts with perfectly articulated, intelligible objects that the mind has little difficulty understanding in a 2-D photo. But mineral specimens have much in them that the mind has trouble figuring out…unless you’ve seen the specimen directly under magnification yourself. And then of course, there are problems like flare and distracting reflections that are not as easy to plan for due to the inverted result. I don’t know if others have any observations regarding stacking software but my next download will be a trial of the pricey Helicon.

Thanks for "listening."

Regards,

Bob Wilken

29th Sep 2015 13:41 UTCHarold Moritz 🌟 Expert

Hi Bob:

1. I have pretty much the same setup you describe. I dont understand what you mean by "inverted images". Is your camera mounted so that the bottom of it is facing away from you? You should be able to just rotate the mounting on the trinocular. But I think to make things easier for you, and eliminate vibration, your camera should have come with a disk of software to download the photos, but also to live view and remote control the camera from the computer (EOS Utility: Control Camera). This way you do not have to look through the camera on the microscope to compose the image and arrange the lighting or touch it to take a shot and cause vibration. I'm using the same lighting with no major issues, just put diffusers on them to reduce glare and bright reflections. Dont mix the fiber optic light with any other source, like daylight, they dont have the same color balance and will produce some images with a strange mix of inaccurate colors. Also, the fan in the fiberoptic light source will also cause vibration and if you can, stand it on a different table than the microscope, or as I have done, put a bunch of foam padding under it to stop the vibration propagating into the microscope.

2. When processing stacks taken through the scope, use the "Do soft stack" option in CombineZP, otherwise you will get blurry areas. I've been using the software for 6 years, and it hasnt changed, you may not be using enough focus intervals, too. But also stacking too great a range of depth can lead to issues also, especially with bright areas. Expose the images so that the brightest areas are properly exposed (not washed out), even if they are not the area of interest, then after stacking, brighten the darker areas in Photoshop (or equivalent) using the "Image - Adjustments - Shadow/Highlights" tool. You will have to do some editing to the images to eliminate edge effects.

I have no experience with the other stacking softwares.

You can take excellent micro shots using extension tubes on the camera, doing away with the scope, but you will not be able to manually adjust the camera focus finely enough as the magnification goes up. So after you get below a FOV of about 2 cm, you will need a motorized camera mounting rail and controller that will incrementally move the camera toward the specimen, rather than changing the camera focus. These units are about $500 new, perhaps less used, and while they work well, I'm told the user interface is not at all user friendly, so I have deferred, waiting for a better, less expensive unit.

Cheers

Fritz

29th Sep 2015 22:56 UTCEugene & Sharon Cisneros Expert

Hi Bob,

I have used the SMZ-2T, as well as more expensive Nikons for microphotography, but never achieved the result that I wanted. Good pictures yes, but not like some of the best that you see on this site. I finally came to the realization that stereo microscopes are primarily designed to look through, not for high quality imaging. The reason is simple... Stereo microscopes, with the exception of some very expensive ones, have relatively low numerical apertures, typically around NA = 0.1. This limits the theoretical resolution of the objective to about 3 um. This will suffice for wide FOVs, but not for smaller FOVs, at high power. I think that if you start at the lowest magnification for the scope, you will get decent images. As you go to higher magnifications, the quality will fall off.

You mentioned a phototube ocular and that would serve two purposes. For and APS-C format camera, a 0.5X lens is appropriate and will reduce the camera magnification to approximately that of what you see through the eyepieces. It also corrects the image for some aberrations and for flat field.

The best imaging setup, as Harold mentions, is with a camera body, bellows and compound microscope objective. This allows the simplest optical train of just one compound microscope objective and a camera body. That eliminates all of the lenses and prisms (about 6) in the stereo microscope optics train. It can also provide higher NA, depending upon the objective, and therefore higher resolution.

My best advice is don't become discouraged. It takes a lot of patience and experimentation to make excellent images.

BTW, vibration is one of the most difficult problems to overcome in microphotography, unless you are using a speed light or very long exposures. That's the subject of another discussion. But, if you use the live view software and go to zoom, you will be able to monitor vibration. If you can discern any movement at all, it's too much. Every improvement in my images now comes from improving the stability of my setup and it's still not satisfactory for high magnification continuous lighting.

Cheers,

Gene

An early image that I made with the Nikon SMZ-2T

30th Sep 2015 03:33 UTCRobert Wilken

Thanks for the useful tips Fritz;and also, Gene, for your observations and kind encouragement.

It will be interesting to find out if the inversion problem is just a matter of reorienting the camera 180°. A friend had made the suggestion a few days ago. By inversion I simply mean that what I see set up through the microscope oculars turns out reversed in the photographic image. I do not get a photo of what I see. And using a Photoshop program to rotate the image doesn’t correct the problem.

With my previous camera and binocular scope I was used to setting up the photo through the microscope oculars. You might think that it must have been pretty awkward to do. But, I was able to remove the camera from the scope very quickly so as to view and set up the shot. Just as easy to replace it and to take the stack using the LCD. When I have tried to use the new camera LCD to set up, everything has to be moved in the opposite direction of what my mind is telling me to do . And of course, due to the magnification it doesn’t take much to “lose” the photographic target or move it out of view altogether.

My initial frustration with the Canon software was that I had just upgraded my laptop to Windows 10. Canon had no software upgrade. So, I ended up purchasing a refurbished laptop w. Windows 7. I haven’t explored the software beyond using the EOS Utility for uploading the photo stacks. I will check out the “control camera” function as you suggest, Fritz. Right now the notion of arranging the photo on the laptop screen seems a bit foreign to me since I haven’t tried it.

As for vibration, I would love to be able to have the F O unit on a separate table but I just don’t have the room. Another negative with the boom is that it and the stand are always in the way of the fiber optic unit. I do have a set of vibration isolation pads that seem to prevent transferal of vibration. Due to the potential for movement by the boom I’ve been using a 10 sec delay to lock up the mirror and then another 10 sec delay till exposure. Once using the live view, I will apparently be able to see vibration at high focus as Gene indicated.

I have seen the horizontal rail motorized setups. The one by Volker Betz posted here on Mindat is quite impressive but also high end. I came across another one complete w. plans, parts list and cost estimates done by a Canadian.

Do Soft stack was the algorithm I most commonly used but occasionally I found Pyramid Do stack or just the Do stack came out a little better. I’m totally befuddled as to why it’s not working for me now. I generally had stacks from as low as 7 up to the mid teens. I simply did the shots free-hand. With the new setup I replaced the Nikon trinoc coarse focus mount with a Sciencescope coarse-fine mount that has a graduated scale. With this I can keep my depth of field changes at regular intervals. I’m getting stacks in the high teens to up to as many as 32 shots! The result has not been for the better. So far this attempt to improve has not paid off at all.

Gene, I don’t have a technical background. I could not explain what an f-stop is, what the ISO function does or what the relationships among all of the various parts are. I have learned most everything by trial and error or by getting a desired result...not be reading "the manual." I didn’t know what “um” stands for or what an APS-C format camera is. Now I do for having Googled them. Never too old to learn. Nice photo. Nothing like color and contrast.

What do you find is the best ISO setting?

I will let you know what happens.

30th Sep 2015 03:43 UTCDouglas Merson 🌟 Expert

I use a Canon T2i and have had no problem running the Canon camera control programs. I have then on a Surface Pro 3 and my desktop.

30th Sep 2015 13:46 UTCHarold Moritz 🌟 Expert

Hi Bob:

OK, you can invert (or flip) the image in P-shop (rather than just a rotation, which obviously doesnt fix it) by going to Image - Rotate Canvas - Flip Canvas Vertical, or Flip Canvas Horizontal, whichever is needed. Dont know why you get the inversion, but this will fix it. You can just do this after stacking so you dont have to flip every image.

I started out viewing the subject with the camera through an ocular, and later, the camera mount on a trinocular. Had all the issues you describe, but like anything difficult, very doable with practice. However, using the live view on the computer is much more ergonomic and you will quickly be glad you can, rather than the old way. And on the screen you can easily see any vibration because the image is huge compared to the view through the camera itself. With live view your hands and eyes are also free to do things like manually tap the scope, or monkey around with the FO illuminator to see where vibrations originate. The computer should also be on a separate table from the scope as it can cause vibration, too. Another thing you can detect easily is specimen drift. Sometimes, especially when using mineral tack to hold a piece at the desired angle, the specimen will very slowly move. You can see this on the screen because the image freezes while the exposure is made and then when it returns to live view, you will see the image jump a little as it "catches up" to the current live position. If this occurs you will need to more securely mount the specimen.

I'm sure you can download from Canon a Windows 10 compatible of their software. I'm still using W7 as I've heard nothing good about W8 or W10, but that's another story.

Those are awfully long delays you have set up for each exposure, and will make stacking shots an eternity. You should need only a fraction of a second for each. Are they shaking the boom, or is it something else?

The number stacking shots you are shooting is typically the same as what I do manually and should be fine, so your issue is apparently not the intervals or the camera.

As far as the technical aspects Gene mentions, read through the camera's owner's manual. Wealth of info in there. But I'll just say when using the camera on the trinocular scope, you will be working with a fixed f ratio, only the exposure time can be varied, and you will see how to adjust that on the live view software. The ISO is the relative sensitivity of the camera. Use a low setting for best quality - I have mine set to 100 or 200. This will result in slightly longer exposure times, but for static mineral specimen photos, that is not an issue. (High ISO settings are best for low lighting conditions and/or fast moving subjects captured by hand-held action shooting out in "the field", which you are not doing here. They increase the graininess or noisiness of images.).

4th Oct 2015 16:43 UTCRobert Wilken

Hi Fritz/Doug/Gene

I just want to let you know that a portion of what you describe in your last message I have discovered from some computer-based research. You know, I never had a course in photography so I have simply been ignorant of simple, basic camera functions: namely f-stop, ISO and shutter speed. Man! YouTube videos are wonderful. God bless the people who seem to enjoy posting them! Once you know there are three ways to increase or decrease light to the sensor, you pretty much have the concepts whacked. I couldn't figure out why the f-stop was grayed out. I reset all the camera settings and tried everything. I finally put the lens on the camera. No problem adjusting f-stop. Well, it finally dawned on me that without a lens on the camera there is no iris, there is no aperture. So, unlike in normal camera use there are only two ways on the scope to manage light to the sensor. Sometimes you can feel pretty stupid! There are no manuals for situations like this. Anyway, that was one hurdle.

The inverted issue was resolved thanks to your suggestion to rotate the camera. It DOES make it difficult to read anything on the LCD but, as you say, the "Live View" software really makes a difference and helps to make things "ergonomic". It's easy to change the shutter speed and ISO right from the laptop. I'm not so sure how many "bells and whistles" will be helpful for the purpose of taking microphotos. One thing I miss is a way to enlarge and sequentially go through the photo stack to review if I want to discard a photo at the beginning or end of the stack (not in the middle for sure). If there is a way, I have yet to find it. Some Sony software has it. Beyond that, all the separate windows that pop up when starting to take the stack photos are not terribly helpful. I usually just send them to the task bar. Now that I think of it, one of those windows might be how to review the stack!!

As for vibration, I must say I haven't noticed any. The one think I DO see at high magnification is the laptop pixelization. It looks like all the pixels are vibrating or quivering. I don't know if this is vibration or if it is an electrical phenomenon. If I could find a way to get my light off the table it would be interesting to see if it's still there. I've got an old D & J 170 unit with 23" dual gooseneck and it's at the limit with the big B & L-type boom vertical and horizontal members. The light just barely fits under the horizontal member.

The most consequential issue I discovered was that (although I thought I did) I did NOT have the camera in M. Somehow I had slipped it into Aperture Priority "next door." So, I think what has been happening is that my stacks have been defective and that Zerene and CombineZP couldn't process them properly. My results yesterday, with Zerene were MUCH better. I will have to reload CombineZP to see if it works for me as it used to.

Doug, as for Windows 10, I contacted Canon (now a month or more ago) and they said at the time they had no update for it. It could be they have one now. Canon Utilities was non-functional with Windows 10 on my Dell. On the HP refurbished Windows 7 laptop I got, it started right up. No problem. I really needed a designated laptop for mineral photography anyway.

Fritz, I guess you use Photo Shop. I've never sprung for the fee. I've been used to using GIMP. I don't know whether there is an equivalent to the "Rotate Canvas" function that you are talking about. Right now, with the camera rotated, I find things MUCH easier to deal with. The fact that my previous camera had a fixed lens, must have made a difference...probably because the light going through a convex lens likely flips the image.

Once I downsize a couple of recent photos, I'll attach them to an update.

Thanks,

Bob W.

4th Oct 2015 17:12 UTCHarold Moritz 🌟 Expert

Sounds like you are making good progress, Bob! Yes, one can learn just about anything these days from Youtube. Your situation was ignorance, not stupidity :-) One can never know everything about everything, hence these forums...I even forgot to mention you should have the camera set to manual. Also, you should set the camera's color balance to the light source you are using with the microscope (and only use type of light source). Put a piece of white paper (not perfect, but close enough) under the scope, take a properly exposed photo, and go to the camera menu to see how to set this image as the color balance (if not obvious, review that section in the owner's manual - likely faster than Youtube in this case). Then take another shot to confirm, it should look white, if it didnt before. You could also leave the camera's color balance on auto, which I find works very well, too, for most things. When using the camera elsewhere, reset the color balance.

Yes, the pop-ups when live view shooting are annoying, but once you minimize them, they stay there. You can review images by opening the pix in their file folder and using Windows photo viewer, or the Canon preview window that pops up when shooting.

The pixel "quivering" you see is normal, the live view is actually a video, not a still image.

I got Photoshop CS3 several years ago fairly cheaply (yes i did pay for a license) and it paid for itself through photo work I actually get paid for. I havent bothered with the upgrades due to the cost, CS3 and CombineZP still do all I need to do. Most similar software may use synonyms for the same functions found in Pshop, so go through all the menus of your software in detail and try a function that might accomplish it, there is almost certainly one.

4th Oct 2015 18:17 UTCFred E. Davis

Hi Bob!

You can use GIMP to flip the image either horizontally or vertically. Go to "Image" in the top menu, select "Transform" and you'll see "Flip Horizontally" and "Flip Vertically" at the top of the Transform menu. If you have an "oops" moment and flipped the wrong direction, just go to "Edit" and select "Undo" at the top of the menu, or type "control z" to undo. Note that the "Image : Transform" selection also lets you rotate.

Good luck!

Fred

11th Oct 2015 17:50 UTCRobert Wilken

Hi Fritz and others,

Gee, Fritz! “Ignorance”? “Stupidity”? Really? I don’t know which sounds better! Oh, well. We all fall victim to one or the other now and then. When I think back on what I wrote in the first message here, I can assert that I was so earnest about what I thought I knew. I was faulting Zerene for all sorts of imagined things. Now, I must say I’m ready to purchase. It’s a great stacking program once you understand how it works and once your equipment is functioning as it should. The retouch tool is great too…when you learn where best to use it. Thank you for the suggestion to rotate the camera. The up-side-down images were driving me to distraction. This led to the discovery that my camera was not set on “manual” as I thought it had been. The fact that it wasn’t set properly was affecting all possible stacking outcomes. Also, your nudge to use the “live view” capability of the Canon software has made a huge difference.

Due to all sorts of other preoccupations and tasks at home I haven’t had a lot of time to do lots of photos, but the ones I have done show promise. One can always improve. I have attached a couple of photos of colorful material collected ten plus years ago at the Mascot Mine in Gorham, NH. I am now at the same point as I was with my old setup. That is, the point at which the camera, the microscope and the software are functioning properly and in unison as they should; but also, at a point at which one realizes the time consuming and potentially frustrating part of microphotography comes from achieving the right lighting for what is maybe not the most photogenic specimen in the world. Just when you think you have it right you notice flare from a piece of mica that ruins the scene. You adjust for the flare and the lighting isn’t right any more. There are an infinite number of ways a specimen can be oriented or lighting can be directed. And, it’s amazing how few of them are ideal. Perhaps none! Although we would like to think our specimens are all beauties, most of them probably aren’t. The fact is, they are important because they validate a mineral occurrence from a particular locality and for that reason they are important to photograph. The impulse to make a “silk purse out of a sow’s ear” is still there though. It’s inherent in what we do.

So, with that, I guess I would close out the thread “image inversion.” Thanks to all who chimed in.

Bob W.

The linarite/malachite has a fov of 2.3 mm

The linarite 1.8 mm fov

The smithsonite 2.2 mm fov

All photos resized w. Paint to 1000 pixels horizontally.

12th Oct 2015 14:46 UTCHarold Moritz 🌟 Expert

Hi Bob:

So you've passed through the worst of the learning curve and appear to be coasting now, that's great! The images look just fine.

There will always be "flares" and the opposite, but no one will know but you how else the photo could have looked, so do your best and dont worry about it. Besides, it will never look as good as the stereo eye-brain view anyway. How much does Zerene cost?

Cheers

Fritz

15th Oct 2015 04:05 UTCRobert Wilken

Hi Fritz,

Zerene costs $89 for the "Personal Version" (one-time purchase). It's all I need. There's a Professional version ($289) with a few retouch "brushes" beyond the basic retouch tool. There's also an edition called the Prosumer edition for $189. I came across someone complaining about the professional version's price and that it didn't have that much extra to add. Helicon Focus is even more expensive I believe although you can either pay an annual fee or buy it outright.

When you stack with Zerene it's best to run BOTH the P (pyramid) "map" AND the D (depth) "map". The P map produces an image that "is very good at finding and preserving detail even in low contrast or slightly blurred areas....But (it) tends to increase noise and contrast, and it can alter colors somewhat."

The D map "does a better job keeping the original smoothness and colors, but it's not as good at finding and preserving detail." When you use the retouch tool you have the P map side by side with the D map image. You use a "bubble" tool that you can enlarge or make smaller with the mouse wheel. I have found it's most useful to remove halos in dark areas right next to vivid colors (areas of high contrast). You end up transferring the area over which you pass the bubble (without a halo) from the P map to the area with the halo on the D map. It acts just like an eraser-replacer. And, unlike with a clone tool it's not a painstaking process because you don't have to worry about blotting something out unintentionally. But, since reflections and flare are bit more pronounced on the P map than on the D it's best to avoid them so as not to transfer them to the D map photo. I use the D map photo as the finish image before photoshopping.

Another thing I've noticed is that you don't get anywhere near the distortion around the margins of a stacked photo as withCombineZP. All those little gremlins. I've only seen it on the right margin of photos.

There is a "contrast threshold" tool that I'm not so sure is helpful for micromineral photos. It's supposed to remove areas of "noise" which in the case of mineral specimens is often matrix detail (as opposed to your main subject) that you want. I just use the 0.0 value so it affects nothing.

The link will give you a much better picture of how Zerene works:

http://zerenesystems.com/cms/stacker/docs/howtouseit

Cheers, Bob W.

15th Oct 2015 13:35 UTCHarold Moritz 🌟 Expert

Hi Bob:

Thanks for the advice, that's not crazy expensive, so I will put it on my Christmas wish list.

BTW, the strips of mirror imaging (distortion) around the edges of a CombineZP image can be easily removed. Just before saving hit the "Shrink/Expand Active Rectangle" button to the right of "Go" on the tool bar. That should crop out the crap! But you are likely beyond that software now....

Cheers

Fritz

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