Hallo. Sorry to bother but I’m really stuck with importing 3D images (confocal fluorescence microscopy data) from Fiji. I finally managed to open the .raw file without error messages, still I simply can’t see anything in the rendering window. I can’t understand what’s wrong. Please help. Thank you in advance.
please share your data as well as the data parameters to open it.
Hi Mathieu, thank you for your reply. Sorry for coming back late: I have partially solved by Fiji 3D Viewer, however that plugin is rather buggy and I’m not happy with that rendering, I guess one can do much better. So, here is one example of my type of files (one 3D image stack contained in a Leica .LIF project file, opened in Fiji and exported). I have discovered now that Fiji exports to nrrd format, which Paraview should be able to open. Indeed, the file was opened without error messages, but still I’m facing with the issue that I can’t see anything plot in the rendering window… maybe I miss some really trivial option, clicking or checking some box somewhere (sorry, absolute beginner with Paraview…). There should be 3 channels (different fluorescence colors), each 31 slices in the stack, each 1024x0124 pixels. Download link:
https://wetransfer.com/downloads/1e72acab2747670eb578a42f26b141d220240702123230/fea569826b892d64bba0ad8df5bcea2020240702123230/dfbf80
Hi Mathieu. Thank you! I did it, and see the same. However, it is not exactly what I would expect. Maybe I have to set a threshold in intensity only above which some signal is visible (to cutoff background noise in my fluorescence intensity images; I need kind of transparency for all the space of the parallelepiped outside my living cell spots, in white/red). BTW: I have discovered the following tutorial for 3D imaging in Paraview of scientific images representing data of imaging devices (not models for CAD): VR Software wiki - Paraview + Volume Rendering Tutorial . However, I can’t understand where to find and how to install the the VR plugin…
