Use skeleton from catmaid as seed points in MIB

I have generated several skeletons in catmaid and would like to create volumes of the whole neurons in MIB. Is there a possiblity to import the data to MIB so that I can use them as seed points for segmentation?

Thanks,
Stefan

Hi Stefan,
it should be quite straight forward if the skeletons are saved as images (for example, TIFs). These TIFs can be opened as a mask and after that assigned to the Seed material of a model. Add another material for background and run graphcut.
If the skeleton saved as sequence of coordinates, it should be possible to write a script to convert coordinates into the seeds.
In which format you can export the skeletons?

Best regards,
Ilya

Hi Ilya,

I don’t think that I can save the skeletons as an image. My export options, as far as I know, are: SWC, NRRD and JSON.

Best wishes,
Stefan

I never worked with SWC, is it something like text file with numbers, similar to CSV?

NRRD is an image format, you can try to export skeleton in this format and open the files in MIB as mask: Menu->Mask->Load mask->select there “All files” in the filters dropdown (.) and open NRRD file stack.

JSON should also be converted to an image stack.
If you can send me some example, I can check the options.
Also, do you use matlab or compiled version of MIB?

Ilya

The import of the NRRD file via the mask did not work. A colleague of mine will have a look at the JSON file and see how we can convert it.
Corrently I am only using the compiled version but I can change to the matlab one.

I was not able to find any details of nrrd format that catmaid generates. Was there any error message during loading?
If you can send me a small example saved in these formats I can check the import functionality into MIB.

@WeSt,

Consider checking out simple neurite tracer

to convert your swc’s from catmaid to a binary mask, which you can then save as a nrrd (or whatever image format Fiji can write and MIB can read).

See this thread

yup, here’s a too short spec for swc.

John

2 Likes

I have send you a nrrd, swc and json file.

Thank you for your help!
Stefan

Thanks for the suggestion. I tried but, although I updated Fiji, my SNT is an other version and I cannot find ‘Render/Analyze Skeletonized Path’:

Do I need to add some additional update sites?

Stefan

Hi @WeSt, sorry for the late reply. If you have the latest version of SNT (available through the Neuroanatomy update site), you should have the option to skeletonize Paths in the Path Manager, which will convert the selected Paths to a skeletonized image volume. To skeletonize the full Tree, make sure all Paths in the Path Manager are either deselected (not highlighted) or selected (highlighted). Otherwise, only the currently selected Paths will be skeletonized.
skeletonize

Just wanted to mention that in addition to @arshadic instuctions, this can also be tackled programmatically. Please see this post for details.

1 Like