Focus Stacking with a Raspberry Pi – Mould Macro Photography Project

    image 10mm x 10mm sample mold growing on sliver beet root - six days old.
    image  coverage 10mm x 10mm; mold growing on sliver beetroot – six days old.

    In the search for interesting things to photograph on a macro scale using my focus stacker, it was suggested to me by Sara that mould might be worth looking at – well, it is!

    I started off with a 10mm sliver of beetroot less than a week ago and it is already producing lots of mould growth. I placed the piece of beetroot on a small polystyrene foam-board tray in a sealed plastic container and put that in a cupboard where it would be in the dark and stay warm. Within three days I had a few circles of white mould with one starting a grey centre.

    Three days later the surface was covered in interlocking circles of mould – all grey except one which is very yellow. The white/grey mould is like little flowers and the yellow mould is like small pom-poms. It will be interesting to see what happens next.

    I have reproduced some of the images from my focus stacker here. I have some other food items in my test lab waiting to see what will happen to them.

    The image above was taken at a magnification of approximately 0.5 and cropped to show a 10mm sample width – taken with a Tamron 90mm SP lens without extension. Low magnification images were taken with a  Nikkor 50mm enlarger lens at f 5.6 reversed onto 135mm Minolta MD lens at f 3.5 giving a magnification of 2.7 – focus increment of 100microns – varying numbers of images. Higher Magnification images were taken with a Componon 28mm enlarger lens at f4.8 reversed onto a 200mm Minolta MC lens at f8 giving a magnification of 7.1 – focus increment of 20 microns – varying numbers of images. Images were all stacked in Zerene Stacker.

    Click on any image for a slide show of the hidden world of mould (I never thought I would be typing that!)

    Componon 28mm reversed onto Minolta 200mm lens. Focus increment 20 microns, 251 images. Day 3 of mould growth.
    Componon 28mm reversed onto Minolta 200mm lens. Focus increment 20 microns, 251 images. Day 3 of mould growth. No yellow mould apparent yet. Lots of beetroot still showing.

     

    Nikkor 50mm reversed onto Minolta 135mm lens. Focus increment 100 microns, 164 images. Day 6 of mould growth.
    Nikkor 50mm reversed onto Minolta 135mm lens. Focus increment 100 microns, 164 images. Day 6 of mould growth. Yellow mould apparent. No surface of the beetroot showing.
    Componon 28mm reversed onto Minolta 200mm lens. Focus increment 20 microns, 88 images. Day 6 of mould growth.
    Componon 28mm reversed onto Minolta 200mm lens. Focus increment 20 microns, 88 images. Day 6 of mould growth.
    Nikkor 50mm reversed onto Minolta 135mm lens. Focus increment 100 microns, 57 images. Day 6 of mould growth.
    Nikkor 50mm reversed onto Minolta 135mm lens. Focus increment 100 microns, 57 images. Day 6 of mould growth.
    Componon 28mm reversed onto Minolta 200mm lens. Focus increment 20 microns, 133 images. Day 6 of mould growth.
    Componon 28mm reversed onto Minolta 200mm lens. Focus increment 20 microns, 133 images. Day 6 of mould growth.
    Componon 28mm reversed onto Minolta 200mm lens. Focus increment 20 microns, 283 images. Day 6 of mould growth.
    Componon 28mm reversed onto Minolta 200mm lens. Focus increment 20 microns, 283 images. Day 6 of mould growth.
    Nikkor 50mm reversed onto Minolta 135mm lens. Focus increment 100 microns, 100 images. Day 6 of mould growth.
    Nikkor 50mm reversed onto Minolta 135mm lens. Focus increment 100 microns, 100 images. Day 6 of mould growth.

     

     

    Beetroot Mould Componon 28mm reversed onto Minolta 200mm lens. Focus increment 20 microns, 189 images. Day 3 of mould growth.
    Beetroot Mould Componon 28mm reversed onto Minolta 200mm lens. Focus increment 20 microns, 189 images. Day 3 of mould growth.

    Focus Stacking with a Raspberry Pi – New Light Box and Backlight Display

    Green Bottle Fly
    Green Bottle Fly

    I have made great strides in the last week, having devoted a serious amount of time to fine tuning the set up. And now I have been able to produce an image of a green bottle fly that I am reasonably happy with. (see picture on left).

    This was taken using a Nikkor 50mm f2.8 enlarger lens reversed onto a Minolta 135mm MD lens using an NEX7 camera with the new light box and display.

    The focus stacker system
    The focus stacker system

    I am really pleased with backdrop arrangement that I now have operational. It was much easier than I thought. I have had this old PC monitor lying around for some time and now it has a purpose in life!

    I have made a series of colour jpeg images in Photoshop – some flat and some grads. These are in a folder on the desktop and when opened using the windows photo viewer, I have it set up to provide a backdrop of roughly the right size. I can scroll through them to see what gives the best effect and adjust the size of the displayed window to suit the magnification I am using and get the gradient where it needs to be.

    Looking inside the light box
    Looking inside the light box

    The new light box was constructed and tested over an afternoon earlier this week week. It is about half as big again as the original one and is doing a much better job at diffusing the light. Inside there are some removable baffles to limit the back lighting.

    Stacker arrangement with new light box and pc display
    Stacker arrangement with new light box and pc display

    The light box extends further forward than the original one, and so can throw more light on the front of the subject. There are still a few hot spots and I am thinking about an inner diffuser made of white tissue paper like a tunnel over the specimen, to give more diffusion. This is also likely to demand a longer exposure so it will require some compromise.

    Nikkor enlarger lens reversed onto Minolta 135mm MD lens
    Nikkor enlarger lens reversed onto Minolta 135mm MD lens

    Also on my list was to play around with different focus increments on the same subject with the same lens configuration. The jury is still out on that, as it is quite a lengthy process to take the images, then process them and try to evaluate sharpness etc. I am getting there.

    I think that the rig is now 95% of where it needs to be – There are some minor changes required to the software for the Raspberry Pi that would help to speed things up a bit between shots and deal with a few bugs (software variety!) – nothing serious and a job for a rainy winter day.

    Stacker arrangement showing light box platform and lights - set up for double fly shot
    Stacker arrangement showing light box platform and lights – set up for double fly shot

    What now needs sorting out is my ability to prepare the specimens – particularly cleaning, and arranging the legs but there are other things too which I will cover at a later date. I am also looking at optical jacks that come in very small sizes for making minute adjustments to the height of the specimen when on the rig, for accurate framing. There are some relatively inexpensive ones available in the USA (of course) but the required postage to the UK is prohibitive.

     

    Focus Stacking with a Raspberry Pi – initial trials

     

    Green Bottle Fly
    Green Bottle Fly

    I have had some time to play with my macro focus stacker recently, having accumulated some specimens to practice on. And so I have found that I need to acquire a new set of skills besides those of macro photography, namely the mounting and preparation of the insect specimens, and the cleaning thereof. They aren’t exactly dirty per-se, but they have microscopic particles on their eyes and in their hairs that catch the light and/or are noticeable in the image and can be a distraction – awfully difficult to remove, even in Photoshop!

    And it can take ages to get everything lined up exactly as you want, bearing in mind that one is dealing in fractions of a millimeter.  The whole business of mounting and arranging is very fiddly, time consuming and frustrating. If you want a nice clean symmetrical head on image you will have to do some work for it!

    This shot is of a green bottle fly (not a blue bottle). It was taken with a Nikon 50mm f2.8 enlarging lens reversed onto a Minolta MD 135mm lens with adapter on a Sony NEX7 camera. This gives a magnification of about 2.5.  The stacking increment was 100 micrometers. I used Zerene Stacker for processing.

    I have realised I need to do a lot more work on the lighting, as my light box is giving too much back lighting and not enough front lighting. Also I need a better way of providing a coloured back drop. I have an old pc monitor that I may experiment with, by using it as a back drop driven from a pc running photoshop or something like that, and displaying a suitably coloured screen. I am not sure if it will be bright enough, but we will see!

     

     

What’s it all about?

Here are my jottings about my photographic projects and activities. I have been working on a focus stacking macro photography rig. There are quite a few posts about that. In addition I write about other photographic activities as and when!

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