I am trying to produce a 3D reconstruction of histological slides using a software. In order to do so, my slides are to be converted from a generic image to the 'pyramidal' TIFF format. I was recommended to use 'ImageMagick', which enables file conversion. I'm required to input these instructions
However, I've encountered multiple problems.
1. The tutorials online < https://www.youtube.com/watch?v=hy75zatrDcQ&t=683s > show that there is a 'convert.exe' in the file location where ImageMagick is downloaded (Fig. 1), but for the latest version I've downloaded (Fig. 2), the command is missing. I came across a comment saying that it has been removed as the command clashes with Windows, and that is why the command is now 'magick' as seen on the website (Fig. 3).
2. Okay now I know it is no longer 'convert', however where am I to input the command? There is no terminal in the ImageMagick interface (Fig. 4).
Solving this issue can really help me to move along to actually trying out the software itsel.
I am not sure how you installed ImageMagick, so the commands could either be in the path or not.
Best way is to open a terminal in the folder with IM binaries, by pressing left shift and right click in this folder, an option should be there to either open command line or powershell, it's from there you should run IM commands.
(Could also just open command line, Win+R and the type cmd and cd to the appropriate folder.)
As for the command itself I just checked that convert is still available in my linux distro. However, in Windows it would seem you just have to input the desired command after magick.
You might also be better off loading your pyramidal TIFFs into a software more suited for what you want to do. ImageJ is freely available and is more suited for scientific analysis like you are trying to do, and I suspect it could open your files natively.
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