Hello!
I am trying to shift to Vaa3D for tracing but I want to be able to use traces that I have completed previously in the SNT plugin on ImageJ. Currently, whenever I save my traces on SNT as an SWC file and try to open that same file on Vaa3D, I get an image showing a linear bounding box and no traces. How can I view my traces from SNT on Vaa3D? I have attached a screenshot of the 3D viewer without the axes when I try to open the file and as you can see, the bounding box is linear with no traces inside.
I have tried converting the SWC file to an ESWC file and I have also tried sorting the SWC file (I don't know what that does exactly but I thought I might give it a try). Neither of these things have worked. I also had the software check for updates and it says that "Your Vaa3D is NOT older than the current binary release. You do NOT have to update for now." Some help would be greatly appreciated!
Hello!
It may be revevant with your swc file (may be some space mode), you can attach an example of your swc file to me, then it will be much easier to find why this happened.
Best wishes,
Lingli
Hello Lingli!
Here are my SWC files from a single neuron from SNT:
The following messages include the remaining SWC files since I couldn't submit them onto a single forum post
Originally posted by muhibmethani:
The following messages include the remaining SWC files since I couldn't submit them onto a single forum post
Originally posted by muhibmethani:
Originally posted by muhibmethani:
The following messages include the remaining SWC files since I couldn't submit them onto a single forum post
Hello! the question is solved. you should remove the extral spacing in the swc file, then you can open it in Vaa3D (use CTRL+L can help you see more clearly ). You can use find and replace function for single swc or write a script to replace the large spacing. the following attachment was an swc file after removing the large spacing. Best wishes, Lingli
Originally posted by Lingli Zhang:
Hello! the question is solved. you should remove the extral spacing in the swc file, then you can open it in Vaa3D (use CTRL+L can help you see more clearly ). You can use find and replace function for single swc or write a script to replace the large spacing. the following attachment was an swc file after removing the large spacing. Best wishes, Lingli
Hello Lingli,
To remove the extral spacing in the swc file, is the "find and replace" function a plugin in the Vaa3D menu? I can't seem to find it. If not, how exactly did you remove the extral spacing?
Also, how would I go about opening SWC files generated from Vaa3D in SNT? Whenever I try and take traces that I have done in Vaa3D and open them in the reconstruction viewer in SNT, it appears that the Vaa3D traces are magnified. How would I get rid of such magnification?
Hello,
the easier way to remove the extra space , you can open swc file as txt file ,then you use the find and replace function and do it.
Best wishes
Hello,
you can refer to the screenshot (attach file) below.
Originally posted by muhibmethani:
Also, how would I go about opening SWC files generated from Vaa3D in SNT? Whenever I try and take traces that I have done in Vaa3D and open them in the reconstruction viewer in SNT, it appears that the Vaa3D traces are magnified. How would I get rid of such magnification?
Hello,
I will try SNT and give you an answer one-two days.