![]() ![]() ![]() However, the actual operation is done by a so called “Blitter”. If you want to dig a bit in the code to find out what the Image Calculator is actually doing, the Image Calculator code is online. I would raise another question: How do you know that the intensity in both channels is really the same? I assume the channels express intensities which were imaged with a different wavelength, right? How do you justify subtracting an image with wavelength X from an image with wavelength Y? Maybe a reviewer could raise such a question… Thus, in your particular case, 32-bit images should be preferred from a mathematical point of view. However, 8-bit images don’t support negative values and thus, the result would be 0. For example, if you work with 8-bit images and you subtract a pixel with value 8 from a pixel with value 7, the result should be -1. However, it depends a bit on the image type you are working with. The other other option for me is to manually look into the code. If anyone has any deeper understanding of the image calculator I would be most appreciative. the latter determines whether I need to come up with a new analytical strategy or not. Is it literally subtracting the intensity values per pixel from image1 and image2? Or is it removing any pixels that are fluorescing in one image but not in the other according to some threshold? Wether it is doing the former vs. On the documentation for ImageJ, it simply states that an image calculator subtraction is Image = Image1 - Image2, but that doesn’t give me enough information for a publication. Since the final channel (after the “Image Calculations”) is what I will be measuring intensities from for publication, I need to know precisely what the “Image Calculator” does. With the second channel, I subtract the first (generating a new channel with everything BUT the protein of interest), which I then subtract from the original channel. I found a way to remove this non-specific labeling by doing some fancy work with the “Image Calculator”, since another channel also co-labels the same cells. However, there is some non-specific labeling of the antibody I used near the top of the confocal stack, which is not due to the antibody binding to the protein of interest. I want to essentially measure the fluorescence intensities of cells in one channel using the “measure” command via hand drawn contours. So it really does not matter much how old the core installation is, as it can be updated online.I have a few confocal stacks that I need to analyze for a research project. Regarding updates, if you download a couple of years old Fiji installation you can just use the built-in updater for the plugins you need, also for the ImageJ 1.x layer. So there is really not any need to choose any fixed path just use the solution that fits your workflow best, and you can change it later. That goes the other way too nearly everything you develop for ImageJ 1.x will also work in Fiji. Nearly everything that works in Fiji will also work in ImageJ 1.x if you use Java 8 and include the dependency libraries. I work with materials technology, so I prefer to develop my workflow in ImageJ 1.x, and rather move the few plugins I need from Fiji over to my ImageJ 1.x based installation. It loads and runs much faster and is much simpler to use for a non-programmer, since you can just use the “Compile and Run” feature for plugins without any need to learn or understand an code-management system.Īlso, most of the plugins in Fiji were written for bio-sciences and have limited usefulness outside that field. I use both ImageJ 1.x and Fiji and by far prefer the former. Software is preferrably slim, but why choose an inferior piece of software just because it’s “slimmer”? Nobody is running this on a 20 year old machine anyway, saying “oh well, looks like I can only use the inferior ImageJ1 because I can’t be bothered updating to a machine only 15 years old I found on craigslist for free”. One or more software developers invest countless hours of precious time into it. I can’t really understand the “use ImageJ1 if you like slim software” argument. Why would anyone keep updating ImageJ1 (in fact it appears to be updated more frequently than Fiji, at the very least with stable public releases, Fijis latest one is almost TWO FRICKING YEARS OLD!)? Why not have ONE piece of software that includes everything someone might need? Is there anything in ImageJ1 that is not in ImageJ2? Or vince versa? If so, what is the excuse for the other piece of software not to include that new feature? Nowhere you can find information on the actual differences. Just starting with ImageJ and seriously confused. ![]()
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