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cortex-lab / Suite2P

Tools for processing 2P recordings
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Using mRuby channel to register GCaMP channel #98

Closed ghost closed 6 years ago

ghost commented 7 years ago

Hello,

I am new to this software. We are using mRuby-P2A-GCaMP6 to visualize the activity of neurons in prefrontal cortex. In our experiments we have a really bright red channel (mRuby, cytoplasmic fill, but no activity) that we would like to use to register that same channel and a second channel that has the GCaMP signal. In the experiment the green and red channel are in the same cell. Is it possible to do this with this software?

Thanks in advance.

hwpdalgleish commented 7 years ago

Hey,

By register, do you mean on a given day register all frames for the dataset for motion correction? Or are you talking about registering entire movies across multiple days to track cells over time?

Henry

ghost commented 7 years ago

Hi Henry, I meant on a given day register all frames for the dataset for motion correction.

Thanks,

Alberto

On Oct 11, 2017 6:07 PM, "Henry Dalgleish" notifications@github.com wrote:

Hey,

By register, do you mean on a given day register all frames for the dataset for motion correction? Or are you talking about registering entire movies across multiple days to track cells over time?

Henry

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carsen-stringer commented 7 years ago

This is implemented for single day registration, the option is 'AlignToRedChannel'. Set ops.AlignToRedChannel=1 to align to the red channel. Also, the script assumes that the red channel is the second channel. If this is not true, then also set ops.rchannel = 1.

ghost commented 7 years ago

Great, we will give this a shot, thanks for the info. - A.

On Oct 11, 2017 6:18 PM, "carsen-stringer" notifications@github.com wrote:

This is implemented for single day registration, the option is 'AlignToRedChannel'. Set ops.AlignToRedChannel=1 to align to the red channel. Also, the script assumes that the red channel is the second channel. If this is not true, then also set ops.rchannel = 1.

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