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Nikon D5000 and microscope

Posted by Jake Trexel  
Jake Trexel December 26, 2009 08:31PM
I attached my Nikon D5000 to my Meiji stereo microscope via a c-mount adapter and t-mount the the camera body. I had the camera on Auto, and it flashed me and said "no lens". I then changed it to manual mode, and I could see through the microscope like I wanted, using live view.
But, when it took the picture, and I wanted to look at it, it was black. The camera gave in a number such as 7/9 and 8/9 but will not show me what I took.

Any idea what I am doing wrong? I am an old timer and Digitals are brand new to me.

Jamey Swisher December 28, 2009 01:10AM
You need to manually set your aperture, shutter, and ISO to get the proper exposure. It sounds like you took a very underexposed image.
Jake Trexel December 28, 2009 04:36PM
Thanks Jamey
That is what happened. I set it to manual, and then I adjusted the shutter speed until it took a good picture and it worked.

Robert Simonoff January 17, 2010 01:56AM
Jamey we are also trying to do micro photography, but our camera is a Canon Rebel EOS. You mentioned "set your aperture, shutter, and ISO." Do you know if there is a way to set aperture when there is no lens? I thought the F stop control was built into the lens itself.

Correct me if I am wrong, but one should use as low an ISO as possible. Then the amount of light for the exposure is controllable by only 2 things really: the shutter speed and the brightness of the light source you use.

Jamey Swisher January 20, 2010 03:46AM
Yes, you are correct. Some adapters though have an Iris for adjusting the aperture basically and some do not. So, yes, if yours does not have an aperture/iris in it then the best choice would be to set the camera into manual mode and adjust the shutter speed or light source strength until you get the proper exposure. Sometimes it is far better to just allow the shutter speed to get longer because you can end up with blown highlights with a stronger light source.

It is also best to keep the ISO as low as possible, yes. It should be safe on your camera and the Nikon D5000 to go up to ISO400 if need be. Use and download the appropriate profile for your camera model to reduce any noise if need be. I find it works best to keep the greatest amount of details while reducing the greatest amount of noise and it is fully tweakable as well which is where its power truly lays. But ISO400 once reduced to internet size shouldn't need much reduction unless you severely underexpose and need to push the exposure in editing. SO keep the ISO between ISO100-400. I believe the native ISO for the Rebel is ISO100 and the native ISO on the D5000 is ISO200, so those are of course your optimal settings where the camera will capture the most details and dynamic range(DR).

Both cameras have the exposure meter/bar in the viewfinder(VF) so keep an eye on it until the exposure is close to the center(zero/0). If your background/base is white you want to underexpose by about .5-1 stop, so adjust shutter or light until your meter/bar in your VF is at the -.5 to -1.0 mark. If your base/background is black you need to do the opposite and overexpose by .5 to 1.0 stops, so you would adjust until your meter is at +.5 to +1.0. This is due to the colors tricking the metering on the camera. The easiest way to do this is to use your camera's exposure compensation which is represented by EV, make sure it is the metering EV and not the flash EV adjustment though, hehe, or it won;t make a difference.

You should set your camera's metering mode to spot meter or center weighted average. I don;t think the Canon has Spot Metering. Even if it does, until you reach the 5D MkII or 1D/1Ds MkIII series bodies the Spot Metering mode is not even a true spot meter sadly. :( But is still the mode you want if you have it.

Your best bet is to pick up an external light meter that has a spot metering mode and use it to meter the light through the scope(some meters even have scope attachments like mine does) and then set the metered settings into your camera.

Your best choice is to also shoot in RAW mode and process your images via a RAW software or Photoshop. This allows for the utmost control, details, and quality, as well as that extra dynamic range(DR) if need be. You could also do a pseudo-HDR image from that single RAW file if you want the extra/high dynamic range(HDR) as well. I prefer Dynamic Photo HDR software for this purpose as it doesn't over process the images like many of the other HDR softwares do. Photoshop also does a decent HDR job but needs far more knowledge on the user's side of things.

Hope this helps. If not please ask any questions and I will be glad to help out.

Registered Gemologist
Research Gemologist
Club President/Owner
Jake Trexel January 20, 2010 06:23PM

What you wrote is the best information I have seen on taking a picture with a Micrscope, and I have been doing since 1986, when I did crystal research for breast cancer. Wish I knew you back then.

Here is my first try, and also using a Paint Shop Pro X, to make the black back ground. I found out due to my spine I have to purchase Nikon's program that will allow me to use my camera with my computer. I can't bend over to see the LCD on the camera.

thanks once again
Dr. Jake Trexel
Rodolphe March 02, 2010 08:22PM

I'm a french researcher working on plankton and I have a new D5000 on my microscope. I don't know why, but I can't get the exposure meter/bar in the viewfinder in manual mode. Could you help me and tell my how I can get the exposure bar ????


Jamey Swisher March 03, 2010 03:52AM
I wish I could help on that one, but I can not, sorry. I don't shoot Nikon now and do not have access to that model. :(

The in camera meters are not exactly accurate anyways, so why not snag a Gossen Luna Pro light meter + Microscope adapter, should be under $100 US for both. That setup is what I use for metering in my scope shots.

Registered Gemologist
Research Gemologist
Club President/Owner
Robert Simonoff March 03, 2010 02:05PM
Thanks Jamey! With your help and that of Frank DeWitt I have my first two micro pictures. Obviously need lots of practice still.

The following was my first one. It was stacked using combineZ. But as you can see there were not enough pictures in the stack. There was also some vibration on the table, so I think I need to retake this.


This one was taken with 20 images in the stack. There is still a issue in that some of the needles are not coming out focused. There are probably other issues some of you could point out.
Nontronite on thomsonite and mesolite from Sugar Grove, VM. FOV 2mm

Although neither is perfect, I am enjoying the learning process. If anyone has recommendations of what else I should be doing and exploring, I love to hear your thoughts. I wonder if Helicon Focus would do a better job.

Maggie Wilson March 03, 2010 02:59PM
Great work, Bob! I am watching your progress with great interest as I hope to be doing some of the same work soon.

I particularly like the second shot - too me, it has more interest visually -

I took the liberty of cropping the photo - might be too much, as that is a personal preference - hope you don't mind!
open | download - Bob\'s cropped.jpg (70 KB)
Robert Simonoff March 03, 2010 05:43PM
Please Maggie - I don't mind at all! I appreciate any thought people have one this. Certainly it comes down to preferences, but ideas and suggestions will never be rejected by me.

I probably need to retake both shots anyway - in the second, the angle is slightly off. You can see that the matrix is slightly blocking the mineral.

Jamey Swisher March 05, 2010 06:20PM
Not bad at all, especially for your first shots! I think they look nice. A little post processing and they could look even better. Try a little local contrast enhancement and Unsharp mask for sharpening as well. You will be surprised.

Registered Gemologist
Research Gemologist
Club President/Owner
Mesbahul Haque April 07, 2012 03:38PM
Dear Sir

I have a Nikon E200 and D5000, Any body can help me that how I can zoom my sample.
Best Regards

Mesbahul Haque
Owen Lewis (2) April 07, 2012 05:34PM
Are you shooting with the camera c/w lens and standalone (macro photography) - or are you attaching the camera body only to a microscope?

If the first, then to zoom you'll need to fit a suitable zoom lens to the camera. For the second, to zoom the view, your microscope must be capable of zooming the image.

What if you have neither a zoom lens nor a zooming microscope? All is not lost because you can load the unzoomed digital images you capture into a software program like PhotoShop, examine the images at any one of a range of selectable magnifications and mark out and crop just the part of the whole image that you want to keep/print/display.

You can, of course use post-camera cropping in association with a zoom capability as well - if you have that capability. If you have both capabilities but only need use one to frame tightly the shot you want, then always use zoom. Especially at the higher magnifications the results obtained should be superior.
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