These are chat archives for thunder-project/thunder

25th
Oct 2016
Boaz Mohar
@boazmohar
Oct 25 2016 00:36
Hi @dk67604 welcome. It seem that you first need to load your data into thunder using data = thunder.images.fromtif(...), see the documentation so that your data loads correctly. Once you have that you would need a reference image, maybe a reference = data.mean().toarray() to start with. Then
from registration import CrossCorr
algorithm = CrossCorr() 
model = algorithm.fit(data, reference)
shifts = model. transformations
registered = model.transform(data)
Dharamendra Kumar
@dk67604
Oct 25 2016 02:42
Thanks@Boaz.. One quick question please correct me in case I raised wrong question, is the registered images can be saved to TIFF format so that after the registration process , these images can be fit into NMF thunder extraction package.
Boaz Mohar
@boazmohar
Oct 25 2016 03:49
@dk67604 I haven't used the option to save to tif, I save my registered images as binary (tobinary(...)). But the output of the model.transform() is another thunder.images object so you can pass it to NMF.
Dharamendra Kumar
@dk67604
Oct 25 2016 05:17
hats off @boazmohar , it worked. Thanks for giving a nice example to demonstrate.
Jason Wittenbach
@jwittenbach
Oct 25 2016 14:29
@WarnWang thanks for catching that. I’ll psh a fix