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Basically you would just keep the appropriate channel for the used filter and discard the other channel/channels. For example if imaging with Ha after reduction you would only keep Red and discard green and blue. my approach is something like this
1. Image capture
2. Reduction as usual
3. Debayer and split each frame into Red, Blue, Green.
4. Only keep the channel appropriate
5. Register and Stack images
6. Follow rest of the processing steps as usual
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