Hello everyone, diatom specialists.
I need a technique, professional method or software for processing diatoms images captured on an optical microscope, which will allow me to eliminate the background and improve the resolution, and see in detail the keys determination.
Thanks in advance to everyone
Hello Mr. Hamadai,
for image processing the tool ImageJ or better Fiji-ImageJ is a good choice. You directly can subtract the background and enhance the contrast in many ways. I also can recommend the split-into-channels-function which allows you to improve details of your image in different color channels and in the end you again can merge all channels. The help-tool of Fiji-ImageJ will provide you with all the necessary information.
Clean the diatom with hydrogen peroxide before going to microscopic analysis (You can use SEM for better resolution images).
Please find the method
Article A rapid cleaning method for diatoms
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Hello Mr. Hamadai,
As alluded to by Jabir, it is crucial to clean the samples. This can be done a variety of ways, I prefer 10% HCl followed by a +30% Hydrogen Peroxide digestion, but there are other methods. Let me know if you would like a detailed operating procedure. Good photos also require the use of a mounting medium with a high refractive index (wet mounts are unsuitable). Naphrax is the best modern option, but I am told cinnamon oil can work in a pinch. I prefer to edit photos using Photoshop. I would probably learn imageJ if I had to pay for photoshop, but I have institutional access. There are a few tricks I know to clean up photos, but I feel that I should specify that, these days it is considered best practice to include background debris. The reason is that the debris in the background makes it hard to hide any alteration to the valve morphology. The best tricks to use are stitching together photos of large diatoms that cannot be captured in a single field of view, and stacking images to get multiple planes of focus in a single image. It may be easiest to run a demonstration of these techniques on a zoom meeting than to write up a step by step procedure. If anyone would be interested, let me know and I will schedule a few demo's. Lastly, for the same reason I recommend including background debris, be careful about how much you edit these photos, apparently there have been some cases of dishonesty. For reference I have included what I would consider a professional quality plate (my microscope was the weakest link in the production of that photo).
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