Modified fluorophore color code #202
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Otherwise these suggestions LGTM! I also noticed that on the new Opencell dataset. Thanks @ieivanov
iohub/display_utils.py
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| "blue": ["DAPI", "Blue", "BFP"], | ||
| "red": ["Red"], | ||
| "orange": ["Orange", "Cy3"], | ||
| "yellow": ["Alexa561"], | ||
| "yellow": ["Cy3"], # Cy3 emission is at 570 nm |
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Since we are at it, should we add the color names as values of the color keys? i.e can we add yellow as an option for yellow and for whatever color?
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Alexa561 also needs to be yellow then.
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If you ask me, I'd keep these default fluorophore colors to the bare minimum. If we start adding esoteric fluorophores, then there would be no end to this. I'd suggest removing GCaMP, mNeon, dTomato, Alexa561, Alexa568, MitoViewGreen, MitoView633, LysotrackerRed, etc. Also, isn't white the default color? In that case, I'd remove that whole key |
Good point. We inherited the 'white' part from the legacy waveorder writer. |
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OK, I've cut down the number of supported fluor to what I think is the bare minimum. Let me know what you think |
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LGTM! |
Suggesting a modification of the display color for some fluorophores.
I found that Cy5 and mCherry were both plotted in magenta, when they actually have quite different emission spectrum.
Alexa561 was also listed under both magenta and yellow colors.