Hi all! Just starting to dig into the uses of CLIJ and CLIJ assistant after #I2K2020. I am working on getting a workflow into CLIJ assistant so that I can look at a few different options in almost real time.
Workflow in a nutshell:
Manually set threshold (3,255 in 8bit images)
Convert to mask and Analyze particles to remove small mask bits
Smooth the image
Run skeletonization and save results.
I am a little bit stuck in the middle with how to work a manual threshold and an Analyze particles… type effect within CLIJ Assistant. I do not exactly need Analyze particles specifically, but I do want something to the effect of “remove every non-touching masked object below 5000 um^2.” There are a ton of options within CLIJ, but I think I have gotten lost in them, even with the search options. Maybe I would need to make a plugin just for that step using many other steps, but that might be a bit overkill for a show and tell.
These are all 2D images, and my current progress looks a bit like this, though I couldn’t remember how to make the processing intensive lines connecting the various windows appear (would it be less intensive if they just showed arrows indicating the direction and the color changed when “updating”).
I have everything working by script, and can process whole folder trees of time lapse images (though I am only using CLIJ for the skeletonization at this point)! I was just wondering if I could visualize the steps and hopefully demonstrate to collaborators why certain aspects of image collection could be important to improve upon. Especially if I can update a manual threshold from 3 to 4 and to 5 within CLIJ Assistant and show the impact downstream when the signal is so faint
It really seems like a great tool for communicating analysis issues with biologists, in addition to the impressive speed-up times.
Is my best option having an intermediate step outside of CLIJ and loading each manually thresholded image into a CLIJ plugin?