Anyone know interesting software for light microscope?
There are proprietary non free software like Nikon’s NIS-Element
Nothing specific come to mind, but…
3D reconstruction from multiple focus layer seems cool.
Image stitching also useful but other FOSS software could do it.
Measuring length, area, etc, could probably use imagej, but imagej UI is very bad imo. (anyone know the state of imagejfx?)
Object tracking, can be done with Blender for example, but would be a pain to switch between bunch of software.
Basic contrast brightness control for live video.
In summary, majority of FOSS can do this, just not in 1 neat package.
Image by me, a hydra. License: CC0
All vendors have their own software packages. In general these are quite good and “user friendly”. Also these programs are optimized for the hardware platform used. I do some confocal microscopy on a Leica microscope using a specialized software for deconvolution and 3D reconstruction. I would never try to do this with FOSS. However, for special analysis I like to use imageJ and a scripting language because this gives me a flexibility that no “specialized” software offers.
The deconvolution we do is on top of a confocal image. It uses algorithms that are optimized for the hardware. The vendor (Leica) put a lot of research in it. So, with only a very limited number of microscopes available, FOSS developers will in general not be able to do this kind of research and develop a similar software.
The 3D reconstruction is just user friendly and works well directly with the original image format. It is also very fast. I could do the same with FOSS but I would just take much longer.
At work I have to use the olympus tool sometimes, and I can say it is only user friendly in quotes. The auto exposure setting is not usable, as it is extremely unsteady, and you cannot switch to useful units that are known from photography, e.g. shutter speed is only available in milliseconds, with a slider control (and a text input field), but a linear slider is rather useless.
Changing measurements in the picture requires to save in their proprietary format, which means I have to work on the dedicated computer of the microscope whenever I want to change something.
There are many more issues, and user friendly is almost exactly the opposite of this software.
Yes, we have an Olympus IX-81 system and the software Cell^P is horrible, at least the old version we use. In contrast the software for our Leica confocal is quite nice.
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