'NoneType' object has no attribute 'selectSlice'

[pinilorenzo]

Dear Devs,

I am currently trying to use abba-python (on Linux 20.04) for registering mouse slices. I followed the instructions provided on the ReadTheDocs (including setting up the environment using Conda). I also downloaded the Fiji (Linux 64-bit) distribution, but I’m unsure how to properly use it or if it needs to be placed in a specific path.

This is my code:

basePath = '/user/images/
myimages = [ '/3994_1.tiff', '/3994_2.tiff', '/3994_3.tiff', '/3994_4.tiff', /3994_5.tiff']
image_mouse = [basePath + section for section in myimages]
aligner.import_from_files(filepaths=image_mouse)
aligner.select_all_slices()

---

AttributeError Traceback (most recent call last)
Cell In[8], line 2
1 #.get()
----> 2 aligner.select_all_slices()

File ~/anaconda3/envs/abba-env/lib/python3.10/site-packages/abba_python/abba.py:450, in Abba.select_all_slices(self)
449 def select_all_slices(self):
--> 450 self.mp.selectSlice(self.mp.getSlices())

AttributeError: 'NoneType' object has no attribute 'selectSlice'

The object passed to "select_all_slices" seems empty.

Indeed, the output of:
print(aligner.mp)
is 'None'

Thank you in advance for your help!
Thanks a lot
Lorenzo

[NicoKiaru]

Hi!

Normally you don't need to install Fiji at all, the repo should take care of it. However, this None exception is not normal.

How do you initialize the aligner ? Don't you have an error message before ?

I do not have a linux machine but I'll try on a VM if you can't find a solution.

Best,

Nicolas

[pinilorenzo]

I’ve transitioned to using the GUI, and everything is working smoothly, thank you!
I now need to download the coordinates of my registered slice in atlas space.
The saved atlas appears to be a 4D image, where the n-th slice corresponds to each input slice. However, I would like to determine the specific space or coordinates in the atlas that each of these slices maps to.

Is there a way to extract this information?
Thank you very much for your support!
Best,
Lorenzo