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NEF showing as Grey 16-bit



I doubt this problem is related to Backyard Nikon, but thought there might be some users here who could help. In my settings I have RAW + JPG saved. Recently after a night out I went to stack my images. Opened first in Sequator to get a quick image done, everything looked good. I then moved to DeepSkyStacker and see that all my RAW files are 16-bit Grey. Opening the NEF file directly from explorer shows it is in color. Back to DSS and any stacked image is essentially B&W. 

So I decided to do trial of Pixinsight, which also opens showing, well nothing. If I open File Formats > Edit Preferences and select "Pure Raw" I will essentially get a pure black image that if I auto stretch I can see the objects, put it is grey scale. 

I don't think this is a BYN issue, but do not know if this is a Nikon issue or Windows issue. I do have the NEF driver installed, and I do not remember updating the firmware on my d5300 since last December. Anyone else experienced similar issue that could share some insight?

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The raw images have not been debayered yet in DSS or PixInsight so they will show up in B&W.  This is normal.

You see the color version of the image in explorer because explorer reads the embeded preview jpg image in the raw .nef file for display, it's not showing the raw data.

Hope this makes sense.

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The JPG version of the Image (embedded in the larger NEF file or solo) is preprocessed In-Camera with strong Gamma Stretch and Saturation in order to make the Output as Colorful as a "standard naked-eye image", while the NEF is left as the RAW Data.

As DSS and PixInsight and Sequator (and other AP Image Processing Apps) work with the RAW Data, until you actually perform the equivalent Stretch and Saturation steps (usually rather late in the processing sequence), the Images will look rather Dim and Colorless.

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