Have run into this on both windows and debian. ![]() Does your macro currently use for loops to iterate the pixels? What sorts of operations are you trying to do? Can you post your macro here, or at least the part doing the pixelwise operations? People here on the forum can help you decide upon and pursue any of those directions, depending on your needs. For example: the Process › Math menu contains several common operations applied to a whole image there are many user plugins for lots of different things if you are willing to dip your toes into the ImageJ2 world, the ImageJ Ops library has quite a few things and finally the CLIJ library lets you run pixelwise ops orders of magnitude faster using your GPUs. There are performant ways to do pixelwise operations in ImageJ directly. So, I wondered how it would be possible to perform the pixelwise calculation in Python, as this is a language that I have been using before.įor that scenario, I think adding Python to the mix will make your life more complicated, and may not be necessary. Ij = imagej.init(‘sc.fiji:fiji+net.imagej:imagej-legacy’) This was resolved with conda init CMD.exe REMARK: when opening the cmd.exe prompt when trying to reproduce the error there was a notification: path not found (in some other words) Installed Anaconda succesfully I opened a CMD.exe prompt.įollowed the instructions under GitHub - imagej/pyimagej: Use ImageJ from Python [EDIT: i got the same notification as described on Github by AdvancedImagingUTSW ( Maven Conflict Yesterday I had a notification that something was wrong with mvn and … I could not reproduce this today. Now my problem with pyimagej and Anaconda: Is this a GUI similar to that of the standalone versions? If so, this would probably fullfil my requirement to re-use the most of my current code. I understand that with pyimagej I can run ImageJ WITH the GUI. I could not find directions on how to use Python scripts within ImageJ/Fiji (also because the site is down…) but I hit upon pyimagej. So, I wondered how it would be possible to perform the pixelwise calculation in Python, as this is a language that I have been using before. So I am looking for a solution where I can hopefully re-use most of the code that I have now. In a part where I need to do pixel-wise calculations with pixels from two stacks this code really becomes too slow. I use ImageJ 1.53b in a Fiji installation. I develop tool for handling a set of image frames. To determine if that is really the case, I will first sketch the original problem that I want to solve and then return to the Python / Anaconda question. It could bring me some nice stuff and then I will go for it. I hesitated to install Anaconda as it adds yet another platform to my toolbox that I have to learn :-).
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