Processing z Stacks 2: 3D Reconstruction & Volume Rendering (FIJI/ ImageJ)
ฝัง
- เผยแพร่เมื่อ 3 ก.ค. 2024
- Learn how to use 3D visualization & animation tools offered by FIJI (ImageJ): 3D Project, 3D Viewer and Volume Viewer. See timeline below.
#FIJI, #ImageJ, #3D, #zstack, #3Dview
In this video:
00:00 Intro
00:10 3D Project
01:42 Interpolation (3D Project)
03:46 3D Viewer
04:57 Animation in the 3D Viewer
06:56 Volume Viewer
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Thanks Johanna for another excellent tutorial.
I’m glad you liked it, @Yasheng Gao.
Excellent tutorial, thank you so much!
I’m glad you liked it. Thanks for watching, @Hannah Shoenhard.
Thansk very much! That's really helpful! I generate the graph I need following your video!
Great Video!!! Thanks for sharing!
Thanks Nicole. I've got other video tutorials (if you haven't seen them yet).
thank you for your great tutorial
You’re welcome. Thanks for watching.
Lovely data set and great video. Surprised it took the TH-cam algorithm so long to show me one of yours.
Thank you so much @Craig Daly. Your videos have actually inspired me to create my own. I owe you a lot.
@@johanna.m.dela-cruz Well done on jumping in. TH-cam needs more of us doing this. Gets a bit addictive though! Lets catch up sometime. C.
@Craig Daly. I would love to collaborate with you sometime. Knowing that our tutorials help people compensates for the hard work.
Super.
Much obliged. Your support means a lot to me.
Thank you for your beautiful presentation. Can you create a video explaining the main differences between z stacks and normal image please?
Hello @Mohammad Khashan. I'll do my best to fulfill your request. Thanks for watching.
Hi Johanna thanks for the tutorial! I was wondering if it’s possible if we do dendritic tracing on the 3D reconstruction?
Hi Patrick. You can do semi-automatic tracing of dendrides on 3D image stacks. Have you tried Big Trace? Here's a link to my tutorial on this, if this helps: th-cam.com/video/Viqf4txCCJ0/w-d-xo.htmlsi=hLOvgfJW5WZRXJEK
@@johanna.m.dela-cruz I haven’t but will definitely check out your tutorial! Thank you so much for the speedy reply, you’re a life saver 🙏 keep up the wonderful work!
Hi Johanna, thanks for sharing this! Could you explain how to do the reconstruction when you have 2 or 3 colors? Should I do this process for each channel individually and then merge them? Thanks in advance!
Hi Roberta Reis. You can do 3D reconstruction on multi-channel image stacks.
Thank you very much, do you know if their's any way to convert the volume into a CAD file ? It would be awesome
Hi @mt.8174. From what I have read, the 3D Viewer can export surfaces as a .stl file, and then loaded into CAD software.
Really great video, thank you for sharing! Sorry for the probably stupid question, but I am new to FIJI/ImageJ and I am wondering what is the extension of the images for the input. I have been trying for a while to find the answer so that I can obtain a volume from a image sequence of png. images so that I can obtain for some features the z coordinate (the height). I have taken a series of images from a CAD model, each one at 30 degrees difference from the previous one, trying to reconstruct by means of 3D Project, but all I am obtaining is a 2D image (like your result in the beginning of the video) with all the images overlaid. I would really appreciate the help. Thank you very much!
Hi @Mihaela Palca. Thanks for watching. Perhaps if you convert your images into 8-bit .tif files, you can then create a stack. Once your images are in a stack, you can reconstruct this. Let me know if you are still having problems. I’m happy to help.
@@johanna.m.dela-cruz Thank you very much for the fast response. I tried to do that, but, unfortunately, I got to the same result as in the beginning - the 2D image overlaid with the other images. I don't know if I am doing something wrong or this is the only result that can be obtained from these images.
@@mihaelapalca1198 There must be something that's missing in your procedure....could you perhaps, send me at least 2 of your images, so that I can try to reproduce your issue? You can send them to me via my email (see About info in my channel).
@@johanna.m.dela-cruz Thank you very much again! I will send you an email today, very soon. Have a great day!
Hi dear Johanna, thank you so much for the video. Even if I applied all steps in the video, I am not able to perform. The Image J says "stack required". Is there something wrong with the data exporting? Thank you so much.
Hi there! You will need a sequence of images from optical sections that were put together as a stack.
Thank you so much for sharing your knowledge ;)
I am currently looking for a tutorial to reconstruct raw cone beam computed tomography images. I saw your tutorial on reconstruction however it doesn't work with my raw images, the image stays the same. I am trying with astratool in matlab however not with sucess. Do you recommend any imageJ applications?
Hi @amandacandemil7861. CT images would have to be reconstructed a different way. There are many other software that can do reconstruction of CT images, but if you want to use Fiji to do this, watch this tutorial:
th-cam.com/video/dCp0RXQIolQ/w-d-xo.html
Hope this helps.
@@johanna.m.dela-cruz I already tried that but unfortunately did not worked. Can you suggest another software?
@@amandacandemil7861 You can try Horos or Osirix , Dragonfly, or Avizo. Hope you find a solution.
My 'Slice spacing (inches)' is at 0.01. Is it possible to change it to microns, please? As I feel I am losing quality in my 3D Projection.
Hi. If your image is already calibrated, go to Image- Show Info and change the unit from inches to microns. The pixel size values you have should automatically change to correspond to the micron scale.
My volume viewer doesn’t have the options you have even though I updated it. You have alpha offset and light options . I don’t have that
Hi Ibrahim. Alpha offset and light options only appear if the Mode selected is Volume (4). Alpha offset is available at these modes: Maximum projection (2), Projection (3) and of course Volume.
Is it somehow possible to create multiple different voxel depths within one Stack? In case the pictures weren't taken in regular distances from each other.
Hi Jo. Once the images are in a stack, there would only be one voxel depth in the image information...unless of course, it is not spatially calibrated, in which case, everything would be in pixels. You can set a single voxel depth, but not multiple ones.
@@johanna.m.dela-cruz Thank you very much for your answer, that's unfortunate. Do you might know als an alternative a way that let's you combine objects and interpolates the space in between?
@@joheer4692 You could probably combine your images as a stack, then 'Resample isotropically' via TransformJ (Rotate).
Hi JOHANNA, I NEED CLASS SEGMENTACION LEUKOCYTE CELL ...
Hi @Paul Avelino Callupe. I do have more tutorials on thresholding and segmentation. Please check them out. Let me know if there’s anything FIJI-related I can help you with.
Do you have experience with bonej?
Hi @J H. I haven't tried BoneJ yet, but this is something I'm planning to work on.