Explorable Microscopy: What is it? How can I make my own images?
The Explorable Microscopy project enables new science, research, and discovery by providing the ability to effortlessly explore microscopic detail across entire subjects and specimens.

 The technology provided here enables researchers, educators, and the general public to:
    1. Capture macro and microscopic images using specialized hardware and software.
    2. Assemble the images into a seamless gigapixel image.
    3. Upload, share, and view the seamless image online at GigaPan.org or on your own website.

Applications advanced by explorable microscopic imaging technology include diverse research programs ranging from cancer research, to museum collections archiving, to archeology, to health lab diagnostics, to food safety inspection methods...virtually anything that requires highly detailed information from small subjects and specimens to be explored and shared.

To make your own images, view the information about the hardware options, open source software provided here, and the process of creating an image. Specific technical information is provided in the Wiki for this site at the Explorable Microscopy Wiki page.



Featured Image:
New Research and Exploration of Tharsis dubius, a fossilized fish from the Upper Jurasic Period (~150 million years ago).





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  • Make a low cost macro rig! How to take a macro gigapan with a few pieces of wood I like complicated things but you can explore the macro world with a few pieces of wood and ...
    Posted Jun 30, 2011, 8:30 AM by Rich Gibson
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Collaborators
Explorable Microscopy is a collaborative project based on the technology and development work by Gene Cooper from Four Chambers Studio / GigaMacro and Randy Sargent, Rich Gibson, Jay Longson from GigaPan.org.

For a complete list of collaborators and contributors, visit the Collaborators page.

GigaPan
Carnegie Mellon University, Create Lab

Four Chambers Studio

  CMNH


Make a low cost macro rig!

posted Jun 30, 2011, 8:23 AM by Rich Gibson   [ updated Jun 30, 2011, 8:30 AM ]

How to take a macro gigapan with a few pieces of wood


I like complicated things but you can explore the macro world with a few pieces of wood and a little bit of patience. Here is the 'simplest least useless thing' for Macro imaging (Thanks jo!).

The zero out of pocket cost macro capture rig
data


For our purposes a 'GigaPan' is:
1) a way of capturing a mosaic of images
2) software to stitch those images into one large image
3) a web site where you can share and explore high resolution images.

It doesn't really matter how you get from the image in your mind to (gigabytes) on the GigaPan web site.

We have been thinking a lot and working on devices to capture images at the macro and micro scales, using CNC techniques, and stepper motors and arduinos and GCode, and lots of fun stuff.  But see #1: all we need is a way of capturing a mosaic of images.  And there is no reason why that 'way' has to be automated.

Enter the heroes of this story: a few chunks of wood.





Modern digital cameras have fantastic macro capabilities, with an ability to focus on objects down to 1-3 cm from the lens.  There are two 'problems' with macro photography.  The first is that you want to see all the details while still seeing the full subject, and the second is the limited depth of field of close up photography.

Stitching together a mosaic of images allows us to capture the full subject at full resolution.  And a couple of pieces of wood can serve as a guide to allow you to take multiple images and then stitch them together so you get a full subject with the ability to zoom in to the smallest details.  

The depth of field problem can be partly managed by being attentive during the image capture stage, or eliminated with Focus Stacking techniques...to be covered later.

 

The trick is to lift the camera just enough so that the tops of your subjects are at the minimum focusable distance, and provide a platform where you can slide the camera and take pictures. You want to make sure that you hold the camera high enough that it doesn't run into the ground when the lens extends.

For the Canon G9 I was able to use material on hand.

Assemble a Frame

I have a number of pieces of 2"x2" wood which are predrilled with 1/4" holes (it was part of my one time fixation with 'Gridbeam' or 'Boxbeam' construction). So when everything looks like a wood frame, use the wood. 

This rig holds the camera a tiny big higher than it needs - if I move it down a hair I would get slightly more zoomed photos.  Also I am limited right now in the number of images I can capture.  The wood cross piece runs into the right side stopping me from capturing another row, and the camera hits the cross piece on the left so I can't go that way.

But the nifty thing is that this rig actually works!

Attatch the Camera

The camera is held in place with a 1/4" x 20 bolt.  I used washers as spacers to make up for the bolt being too long.
The second 2x2 has the sole purpose of being a pointer to the alignment marks on the frame.

Calculate your field of view and how far you need to move the camera

The panorama stitching programs work by comparing the overlapped areas of images
and finding common points.  So you need to move the camera between each picture.
If you move it too much you won't have enough overlap, and the software has trouble
finding common features.  If you don't move it enough you end up with extra overlap
which slows the stitching. 

We want to move the camera so that each picture has about 30% overlap with the 
picture before it.  But how much will that be?  We need to figure out what the Field of View
is of a single frame.

Set your camera up in the rig and take a picture of a ruler.  Go ahead and take a picture
of the ruler both horizontally and vertically.

Macro Calibration Macro Calibration

This shows that we have a field of view about 6 cm wide by 4.6 cm high.  To get 30%
overlap we want to move about 3 cm vertically between each row, and about 2cm horizontally 
between each column.

You can attach a ruler to each side of the rig, or I just marked off intervals of 1/3rd of the field
of view horizontally and vertically.  

(note: you can see obvious 'Barrel distortion' in the ruler images.  It appears that the center is more magnified than the edges. This is especially common on close up and wide angle images.  Fortunately this distortion is quadratic, which means it increases as the square of the distance from the center of the image.  This is the area of the picture which is subject to 30% overlap, and the overlap, combined with clever projection tricks by the software (search for 'SIFT,' 'Projection,' and  'AFINE Transform' for some of the nifty things which make this better).

Macro rig 
This image shows tick marks every 2 cm wide, and every 1 1/2 cm high. Each time you move the camera in a column you move two tick marks down, then move back to the top and over two tick marks.

Using the rig!

  • Find an interesting subject, preferably flat.
  • set the rig over the area of your subject
  • Turn the camera on, set the white balance, set the focus mode to 'macro' (usually by pushing the button marked with the pretty flower)
  • Line the cross pieces up with the hash marks as close to the upper left of the rig as you can get
  • Try and take a picture.  If the picture looks good, great!  Otherwise consider using manual focus as appropriate for your vision, so that you can choose what is going to be in focus.
  • Make sure to shade the subject of each photo.  Just squatting between the sun and your rig will probably do the right thing.  The camera and wood pieces cast shadows, and if all of your images are half in shadow and half in full sun they will not stitch.
  • After each picture slide the camera down 2 hash marks (or however you marked your rig!)
  • When you get to the bottom of the column move the camera back up, then move it right two hash marks.
  • Repeat until the camera is at the bottom right of the frame.
  • You might consider putting something in as a scale bar.  I've been using coins. I have not yet been using coins which my friends at Hackerbot labs shrank with their  15,000 Joules magic coin shrinker.  That would be worth the lulz.
Now stitch the images...If you have GigaPan Stitch, or AutoPano you are good to go.  Otherwise take a look at the (tk) tutorial on using free software to stitch images.



Focus Stacking

This image shows the chaos we experience when we try to focus on everything!  A normal
photographer would have been forced to select their focal plane, say the tops of the plants,
and then that plane would be consistently in focus across the image.

But because this image is made up of multiple images I was given a frame by frame choice of
what I wanted to have in focus. The result is a strange jumble, the in focus area jumps up and 
down in the image, tricking the eye.  We are used to judging the depth of a photographic subject 
by differences in focus, so when the focus jumps like this is evokes a near Escher like confusion.

One answer to this is to use Focus Stacking techniques.  Take multiple images, changing the focus slightly
before each image, and then use software to stitch all of those images into one final fully in focus frame.

And then stitch the mosaic of frames to make a fully in focus final print.

But that is for later...for now, go out with your sticks and bolts and a camera, and take images of flat things, or else, play attention to the focus, and use it creatively!


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