>Do anyone know of a reliable way to merge a transmitted light confocal image
>in grayscale with a lookup table colored confocal fluorescence image so that
>the colored areas of the fluorescent image are mapped on top of the
>grayscale image?


Hi Brett

As mentioned before, there's a number of ways to do this, the most
flexible tool being Photoshop (V4 or later).
Here's a simple, non-destructive (i.e. no permanent changes to the
original material!) and flexible way:

- Open both images in Photoshop
- If the DIC image is in grayscale, change it to RGB Color mode
(Image/Mode/RGB Color).
- Go to the pseudo color image, Select/All and Edit/Copy
- Got to the DIC image and Edit/Paste
- In the layers palette (if not visible -> Windows/Show Layers),
change the mode popup menu from Normal to something else. Recommended
choices: Color, Soft Light, Overlay or Screen. (You can also change
the opacity settings if you like).


Optional:
If you want to adjust the brightness or contrast of either layer,
- select the layer in the layers palette
- create an adjustment layer for it (Layer/New/Adjustment Layer...)
- choose Levels (or Curves, or Brightness&Contrast, depending on your
personal preference) and check  [Group with previous layer]. Click OK.
- Change the scaling (and gamma) to your heart's delight. Click OK.

This, too, is non-destructive, i.e. you can always change the values
(double-click the b&w circle) or simply switch the adjustment layer
on and off in the layers palette.

You can automate all have this and do batch processing when learn how
to create "Actions" in Photoshop.

If you want to go further than that, i.e. if you want to use
selection with tolerance etc. as proposed by Christophe, I recommend
you learn working with layer masks, so you can do this in a
non-destructive way too. However, be aware that this is a bit
"unscientific" as it means manipulating (arbitrarily) selected parts
of your data. In contrast, the methods outline above apply the same
math to the whole images regardless of content, so they do not
introduce a personal, content-specific bias.


Have fun playing  :-)

Beat


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