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cortex-lab / Suite2P

Tools for processing 2P recordings
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Redefine channel order #162

Closed OmriG87 closed 5 years ago

OmriG87 commented 5 years ago

I have many large tiff files that I would like to run through the suite2p pipeline. However the stable red channel is channel 1 and the functional green channel is channel 2. The assumption for registration is that the red channel is last. Is there a way to overcome this?

carsen-stringer commented 5 years ago

You have set ops.AlignToRedChannel = 1 and it does not work? In theory it should work (also set ops.gchannel=2 and ops.rchannel=1 and ops.nchannels_red=2).

It definitely works in the python version - and if you're just getting started with suite2p I'd highly recommend using that over the matlab - we are no longer updating the matlab version. the option is 'align_to_chan': https://github.com/MouseLand/suite2p/wiki/Registration. Also you don't need to be familiar with python, you can run the pipeline through the gui: https://github.com/MouseLand/suite2p/wiki/Run-the-pipeline

OmriG87 commented 5 years ago

Thank you, this worked. I rather keep working with the MATLAB version for now but I will keep in mind the option to switch.