after motion correction extracting data in tiff format

[Marta Gajowa]

Hi,

I started to play with sima tutorial. Is it possible to extract data after motion correction in tiff format instead of pkl or csv?

In lab we used to ImageJ and I wanted to see 'by eye' how the motion correction works.

best,

Marta

[Christopher Snyder]

Hi again Marta,

I use 

....

C=motion_model.correct(...) #motion_model is something like HMM for example

myarray=C.sequences[0].__array__() #you can also call numpy.array() on the sequence

from skimage import io

io.imsave('myfile.tiff', myarray)

You may still have to do StackToHyperstack in imageJ if your image is 3D.

Best,

Chris

--
You received this message because you are subscribed to the Google Groups "sima-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to sima-users+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sima-users/af7b4504-dfe9-43a0-9295-115b868cfdcc%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.