For the best results for press, you should use two images on top of each other... the black lines should be high-resolution line art (1200 dpi is a good setting) overprinted on a 200-300 dpi colored image. This way the lines will be crisper, and the file sizes will be manageable.
1. Scan the line art at high resolution (600 minimum, 1200 preferred) as a bitmap, i.e. black & white only -- not grayscale (unless you have grayscale in the drawings) Under image -> mode you should have it set to Bitmap. If you scanned with grayscale, use 50% threshold to convert it to bitmap. Save this file as a tiff... call the file "page1_lineart.tif" or something similar.
2. Under image -> mode, change to grayscale.
3. Under Image -> Image Size, change the resolution down to 200 or 300 dpi... make sure the "resample" checkbox is checked.
4. Under Image -> mode, change to RGB, or CMYK.
5. In the "layers" palette, double click the "background" layer. Click "OK" to make the scan a new layer.
6. In the layers palette, set the blend (which says "normal" in a popup) to "multiply."
7. Make a new layer with layer->new->layer or in the layers palette... the default name is "Layer 1."
8. In the layers palette, drag the new layer underneath Layer 0.
9. You should now be able to select your colors and paint onto Layer 1. The "multiply" setting on layer 0 will make the black "overprint" onto the layer beneath. (This will be a good preview of what the final print will look like.)
10. Delete the line art Layer 0, then save the colored part as "page1_color.tif" (or JPG).
To composite the images, in your favorite layout program, import the colored image, import & place the black & white image on top, set the black & white to "transparent" or "overprint," and align the two images in the center. (You can accomplish this even in MS Word). This will result in the best quality press-ready piece. Or, send the images to pre-press to composite.
If you are printing it yourself, a single 300dpi image will probably work... just use the "multiply" method outlined above.
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