By combining multiple images they can significantly increase their Signal-to-Noise ratio. It is this property of median stacking that is so useful for astrophotographers who often need to shoot at higher gain to capture their subjects. This works wonderfully, as noise is random, while the signal should remain constant at a location. This means that values that are spurious or outside of the range will be disregarded. If there are an even number of values, it will average the two values that fall on either side of the middle. Basically, median will pick the value as the number that falls in the middle of the ordered list. Higher resolution, focus-stacked image of catapa pollen grain.A Median stack will give a final pixel value as RGB( 130, 169, 209 ). You can see a lot more detail.Ĭatalpa pollen grain taken with a higher resolution camera. The image below, however, was taken with a point-and-click, 6 megapixel camera down the eyepiece. The images above were taken with a Moticam 2 megapixel camera attached to the microscope to reduce misalignment.

the quality of the camera matters a lot.Aligning images is tedious even with align_focus_stack the better aligned images are to start with the easier they are to focus-stack.400x magnified, catalpa, pollen grain that was focus-stacked by hand with GIMP. The general method is shown in this GIMP tutorial.Īligning images by hand and then selecting the areas to cut out can be quite tedious. GIMPįocus-stacking with GIMP requires opening all the files as layers and adding transparency masks to the layers to leave behind just the areas that are in focus. Focus-stacked image of a catalpa pollen grain using Hugin Tools. Which produces an output file called catalpa-pollen-out-b.tif. The images are stacked together using enfuse (details here).Įnfuse -o catalpa-pollen-out-b.tif -exposure-weight=0 -saturation-weight=0 -contrast-weight=1 -hard-mask -contrast-window-size=9 als_000?.tif This command takes three image files (catalpa-c1.tif, catalpa-c2.tif, and catalpa-c3.tif) and produces three aligned images prefixed with “als_” (als_0000.tif, als_0001.tif, and als_0002.tif). It requires two commands, one to align the images, because focus-stacking requires very well aligned images, and another to stack them together.Īlign the images using align_image_stack:Īlign_image_stack -m -a als_ catalpa-c.tif The method for focus stacking with Hugin Tools is described here by Patrick David and here by Edu Perez. The first was with the command-line programs in Hugin Tools, while the second was by hand using GIMP.

I tried two methods for doing the image stacking. The images are of catalpa pollen grains at 400x magnification, stacked using Hugin Tools. Three images (image 1, image 2, and image 3) are stacked together to create a final, focus-stacked image that is in better focus (has a larger depth of field). In each image the microscope is focused slightly differently to bring a different level of the pollen grain into focus. Images 1, 2, and 3 in Figure 1 show a catalpa pollen grain under 400x magnification. The higher the magnification the less you’re able to focus on at a time. There’s a tradeoff involved when you try to focus on things under a microscope.

Hugin image stacking