Hi Robert @haesleinhuepf
Congrats on the development of CLIJx-assistant. It is a completely game changing plugin.
I want to let you know about three functions that I miss a lot on it, hoping you’ll find time and motivation to include them in future updates (I apologize if some already exists and I don’t know).
(sorting in decreasing order of personal need)
- the possibility to start from two or more images.
- the function CLIJx_visualizeOutlinesOnOriginal();
- the possibility to copy one time point or one channel (or simply, split them).
- Consider a practical example. Imagine I use stardist or ilastik for nuclei segmentation and them I wan to use the nuc mask to access info in a different channel. I can’t start clijx-assistant with both images open… The workaround is to merge both as a z-stack and split later inside clijx-assistant, but would be nice a direct way (that would also result in a cleaner clijjx-assistant generated script).
- CLIJx_visualizeOutlinesOnOriginal() is a great and fast way to check if a segmentation meets our standards. Inside clij assistant you don’t have that choice so I need to generate a ROI and restore it on the original image and do it again for any parameter change. CLIJx_visualizeOutlinesOnOriginal() would result in a faster way given the auto update of the assistant and most importantly it works for 3D.
- I think this one is self-explanatory. Of course I can use Re-order Hyperstack at beginning but it would be easier to have a function to do that.