Unexpected colored pixels after registration

[kevin346-sc]

Hi Chandler,
Thank you for your hard work on VALIS ! I am working on 3D reconstrucion based on a series of IHC stained images. But I am a little bit confused about this phenomenon which only happened after registration, using Qupath for analysing. Even though I used default parameter of initialzing the Valis object, I stiil cann't figure out what's going on? Here is a comparison before and after registration with VALIS.


VALIS gave me a good registration result, but I cann't continue prefectly my subsequent process due to the colored pixels covering origin information. Appreciate your patience and wish for your reply.
Best wishes,
Kevin.

[cdgatenbee]

Hi @kevin346-sc,
Sorry to hear you're running into this issue. Would you be able to share the image and "pickled" valis object (located in the data folder), so that I can try to recreate this? If so, could you please send a link to my email, Chandler[dot]Gatenbee[at]moffitt[dot]org? If the image and/or registrar are too large to send, let me know and I can put together some code to help save only the relevant parts of the images and transforms.

Best,
-Chandler