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DIGITALLY IMAGING PARASITIC HYMENOPTERA (or other small, less interesting, insects)

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Start AutoMontage. This discussion is based on the version 4.0. Significant advances have been made in this version and its highly recommended that you upgrade (I'm not being paid by Syncroscopy). The ability to preview a patch of the image before Montaging the whole image is particularly useful and saves a lot of time in the long run. The alignment algorithm is much better, there were many problems with previous versions in image sets that had minimal contrast levels. The new version all but eliminates these (though the ability to manually enter an alignment value would be very, very, useful..hint...hint). In general then number of montage iterations (tweaking patch size settings etc. at each iteration) needed to get a good final product has been reduced, in my experience, from 3-6 to 1-2. There are several new montage algorithms which may be of use but have not been too useful for us. There is also an enhancement option that seems to mimic some functionality available in Photoshop, these features haven't been fully tested.
Load your image set. You can follow along with this by loading this .zip file of 17 .bmps, each ~6.megs (Warning: the archive ts very large, 110megs).

You can click on the folder in the top left or File->open.
To see your images navigate to the folder they are in then change the bottom most dropdown (Files of Type) to "Images (*.bmp, *.tif)". Your images will appear. Double click on any image in the series and the whole series will open, or click on an image then click "Open".

The montage help has a good explaination of what's going on here. Use "Fit Maximum Size" in general

The new dialog alows you to preview the effect of your montage settings by clicking in the "Preview Montage" box. Do this. A menu pops up. Chose "Montage". This preview window will fill with a small montaged portion.
Test various settings.

Hints:

Fixed or Blended methods generally give you the sharpest results (the better being fixed).
Fixed leaves some artifacts, most of which can be fixed with manually editing.
Blended will blend out and smooth through some artifacts. Unfortunately it can also blend out detail in some cases.
To best test the settings move to a "complicated" area of the picture, for example one with many parts in close together, all of which are at different focal depths. Look for artifacts (see Fig.) Increasing the patch size can remove some of these. Work at small increments (1-5). A good place to work from is along legs or antennae that cross many focal depths. Do NOT seek to remove all artifiacts, this is almost impossible and can be manually done very quickly following the montage process (see below). Also experiment with Speed and Precision, frequently when using the Fixed method Speed works just as well as Precision at lower patch sizes but at higher patche sizes precision works very well.
When your happy with the complicated area click "Scan". Remember that touchups will be made following the montage.
Wait.

You now have a montaged image (in the demo: Fixed; Precision; Patch size= 26).
However, there are still some artifacts:
To get rid of them we clould try another patch-size, but even more quickly we can manually edit them out:

To remove artefacts surrounding your image its best to select background from one of the middle most images. Use the slider to move throughout your image set.
If your not on the Montage images click back on them, then click the pen tool (, its the one with the green line).

Draw patches on your original images corresponding to patches you want to replace in the montaged image. You can draw multpile patches by holding down shift and clicking again. While editing right-clicking on the mouse button provides all the options available to you from the menu bar or menu. To paste the images onto the montaged image right-click then choose "Edit paste polygon".

Call up the depthmap image (View->Depth Map)
Zoomed out our image looks pretty good. But by looking at the depth map its clear somethings are a-miss. The depth map tells us which image in the original series supplied information to the montage image at a given area on the montage image. The grey scale indicates the image, here black is 1, white is 16. If we focus on the head and thorax we can see that there are black and white patches on the grey head (see green arrows). Though the problem is difficult to see when we zoom in the artifact becomes apparent. Find the patch most in focus from the montage series, circle it with the editing tool and "Edit paste polygon" to get rid of the artifact. There are always some artifacts, some difficult to find and perhaps not necessary to remove. Note the background is not really problematic here [montage enhance options can be used to get a more "uniform" background].
The confidence map can likewise used to suggest areas of the montaged image that you might want to check for artifacts.

Once your happy that all artifacts are gone you can save the montaged image set. At any time you can right click on the montaged images and save a copy of the current image. You can always finish off the very trickiest artifacts in Photoshop.

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