||It is rare to get an image into a computer
in a state that it is ready to use. In most cases, you will have
to manipulate it digitally. Although a number of programs exist to
do this manipulation, we use Adobe Photoshop for 2 reasons. One,
it is one of the most commonly available and powerful software packages
available. Two, we have licenses for it. This section is
designed to help you accomplish some common tasks in Photoshop.
Scanning is covered in another section. Basically, You can call the
scanner from the File:Import:Twain 32 menu. At this point, the scanner
software is opened and the scanned images open into Photoshop. When you
close the scanner software, any images you scan in are available to be
edited. You must save any scanned images before closing Photoshop or they
will be lost. The links below will jump you to the appropriate pages.
If you so desire, you can have Photoshop lay a grid over your image.
Sometimes this just gets in the way, other times it is very useful for aligning
an image or for composition. For instance, if you are trying to place an
organism's eye at the intersection of two of the thirds (see
the Aesthetics page) you can set up the grid in Photoshop to use as a guide.
To set up a 1/3 grid:
|1. Open the File:Preferences:Guides & Grids menu
|2. Set the Grid options as shown in the dialog to the
right. There should be a gridline every 33 percent, with 1
subdivision. Choose a color that will work with your image.
3. With the grid in place, you can crop or resize the image to
move the point of interest to one of the intersections of the gridlines.
4. You can hide or show the gridlines from the View menu.
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Cropping refers to making a rectangular selection of an image and cutting
away everything outside of it. In addition to cropping, you can also
resize an image. While cropping does not reduce image quality, resizing
can. You should always try to scan the original image in so that the
cropped image will be close to the required size.
|To crop an image:
1. Use the Crop tool (red arrow) to draw a rectangle around the
area you want to keep (blue arrow)
|2. Use the Image:Crop menu item to make the crop. You can
use the Edit:Undo if the results are not to your liking.
|To resize an image:
1. Use the Image:Image Size menu item to open the image
|First, be sure the Constrain Proportions check box at the bottom
is checked. If it is not, it would be possible to stretch the
image vertically or horizontally by changing either the width or the
height independently. In scientific imaging, you shouldn't be
stretching images. If the box is checked, if you adjust either the
height or the width, the other dimension will be adjusted
| You can resize either based on the image, or on the size of
the print you want to make.
|If you are working based on the image, it is most useful to
use pixels as the unit of measurement.|
|If you are working with prints, it is most useful to work with
inches or centimeters.|
|If you are working with prints, be sure to set the resolution
to that of the printer; in most cases it will be at least 300
|If you will be putting the images on the web,
the resolution should be arounf 72 pixels/inch (as shown).|
|Once the units are set, simply type in a value for either the
height or the width.|
|If the resulting image seems to lose resolution, try selecting
another resampling method (or turn off resampling).|
Adjusting the canvas size increases the background of an image
without altering the image itself. It is useful to put a border around an
image, or to give you a place to add a caption, or to build a collage out of
To adjust the Canvas Size:
- Set the background color to the color you want the added canvas to
- Use the Image:Canvas Size menu to open the Canvas Size
- Set the width and the height that you want it.
- Position the anchor where you want it. In the default,
center position, new canvas will be added proportionately around the
entire image. Choosing one of the outside positions will cause
the added canvas to be positioned on the side away from the selected
block, as indicated by the arrows.
- Click OK.
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Brightness refers to the overall lightness or darkness of an image.
Contrast refers to the difference between lightness and darkness in an
image. An image with pure whites and pure blacks has a lot of
contrast. While the proper brightness is somewhat subjective, there are
some definite criteria for contrast. Both the lightest areas in an image
and the darkest areas in the image should have some details; they should not be
"washed out". Likewise, whites should be white, not gray, and
blacks should be black, not gray or "muddy".
It is important to know that the "gamma" settings of a computer's
monitor (not to mention its brightness and contrast settings) may affect
the way the image is seen on different computers. Also, different printers
will make an image look different. You need to know as much as you can
about the final output device (monitor and printer), make the best choices you
can, test the results, and then cross your fingers.
Although Photoshop can help you improve an image's brightness and contrast,
it cannot replace details lost when an image is overexposed (too bright) or
underexposed (too dark). If details aren't present in the negative or
slide that is scanned, Photoshop cannot restore them. The better you
initial exposure, the less you will need the tools in Photoshop to produce an
excellent digital image.
There are several methods to adjust brightness and contrast. You
may find one or more of them easier or more intuitive to learn; also, different
methods may be more appropriate for certain images.
|Method 1. AutoLevels
Use the Image:Adjust:Autolevels menu item to let the computer
make the adjustments automatically. This often works; and not only
does it adjust brightness and contrast, but colors as well. I
think what is happening is that the computer "guesses" what is
supposed to be white and black, then makes those pixels white or
black. Based on what it has to do to make that adjustment, it
changes the rest of the pixels as well. I think. You can
follow this up with Image:Adjust:Auto Contrast, or you can use Edit:Undo
and try something else.
|Method 2. Manual Levels
||Use the Image:Adjust:Levels menu item to bring up the
Levels Dialog. Side the middle triangle (red arrow) to the left or right
to brighten or darken the image. If the channel (at the top) is
set to RGB, you will change all colors at once. You can also select
either the red, green or blue channel to be changed individually; this
will affect the color balance.
|Method 3. Brightness and Contrast Sliders
||Use the Image:Adjust:Brightness/Contrast menu item to
bring up the Brightness/Contrast dialog. Simply move the triangle
to the left or right to adjust the brightness or the contrast.
This is perhaps the simplest technique.
|This is probably the trickiest technique, but it is very
powerful. Use the Image:Adjust:Curves menu item to
bring up the Curves dialog. The "curve" starts off as a
straight line. Move the line up and things get brighter; down and
they get darker (the y-axis controls brightness). The x-axis, on
the other hand, controls what pixels are adjusted, with darker pixels to
the left and lighter ones to the right (this can be reversed by clicking
on the double-headed arrow under the graph). Clicking on the curve
"anchors" that point (a small square is set down). You
can also drag the line up or down.
||The curve above has been anchored at either end, in the
middle, and at one point in the lower half. The top of the line
has been lowered, and the bottom portion has been curved up. The
net effect is to dampen the whites (preserving details in the highlights
of the image) and boost the darks (lightening them). While the
other techniques above generally have the effect of changing all pixels
the same amount, the Curves dialog allows you to adjust different pixels
in different ways. This allows you to control contrast and
brightness at the same time. If you learn to use it correctly, it
can be a very powerful tool.
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As with brightness and contrast, there are several ways to adjust colors in
Photoshop, and once again, the best method to use depends on your intuition and
the nature of the image. Before adjusting color, there are several things
you should realize.
First, there are different ways of representing color on a computer.
Most computer monitors (and TV monitors as well) create colors by combining red,
green and blue in an image. This is the so-called RGB color space. Each
pixel is assigned a number for each of the colors from 0 to 255; the higher the
number, the more of that color. The table below gives the combinations required
to make the colors red, green, blue, black, white and yellow. In addition,
the Color Picker from Photoshop is shown. In this example, the RGB
colorspace is circled in green, and the yellow color being picked is circled in
yellow. This particular yellow is made up of 210 units of red, 254 of
green, and 1 of blue.
|Color on Screen
There are other color spaces as well; printers commonly use the CMYK color
space (Cyan, Magenta, Yellow, Black). If you look in the Color Picker, you
will see that the yellow being chosen is 24% cyan, 0% magenta, 95%yellow (big
surprise!) and 0% black.
there are several ways to select a color to draw lines or add text with
|The foreground color is shown in the box indicated by the
red arrow at left (the color of the box is the color that the text
or lines will be). |
|The background color is shown in the box indicated by the
blue arrow. The background color is what you will get if you
erase the image. |
|You can swap the foreground and background colors by
clicking on the double-arrow indicated here by green.|
|You can open the color picker (see above) by clicking on
either the foreground or bakground color boxes. The color in
the selected box will be replaced by the color chosen with the
|You can choose a foreground color by using the color dropper
on the toolbar (yellow arrow). Click on the color dropper,
then click on a pixel of the color you want in your image (it helps
to zoom in first). If you miss, try again.|
|To change the background color with the dropper, reverse the
background and foreground colors (green arrow), then use the
dropper, then reverse the foreground and background again.|
Adjust Color Balance
|To adjust the color balance, use the Image:Adjust:Color Balance
menu item. In this dialog (see right), you adjust the 3 sliders in
either a positive (right) or negative direction. The colors on
either end show the colors to which the image will be shifted. In
the example at the right, the image will be redder and bluer, but the
green colors will shift towards magenta. Note that this setting
will apply to the midtones; at other times you may want to click on the
shadows or highlights to adjust them individually.
|Method 2. Adjust Variations
||To adjust color using the variations dialog, choose Image:Adjust:Variations
from the menu. At the top, you see two images, one of the original
and the other showing the current pick. Below, on the left are
seven images, showing the current pick and 6 replicates. Each of
the replicates is the original shifted to one of the RGB colors or their
complements. To the right of these images are 3 more showing the
current pick and one step lighter or darker. Once again, you will
note that these changes are being made to the midtones; you could select
shadows, highlights or saturation just as easily.
|To change color, simply click on the modified image that
looks the best to you. This will become the current pick; all of
the other images will then adjust in reference to that. You just
keep clicking until it looks right. If you mess it up completely,
hit cancel then reopen the dialog. Using the lighter/darker
portion of the dialog becomes yet another way to adjust brightness.
|We have already discussed how to use the Adjust
Curves dialog to alter brightness. In that case, we altered the
RGB channel. You can also use the Curves dialog to adjust
individual colors, red, green or blue using similar techniques.
|Method 4. Saving and loading curves
||Suppose you have a number of images which will all require
a similar color correction. For instance, you may have used
regular film instead of tungsten film while photographing through the
microscope, and your images all have a yellow cast. Or perhaps you
photographed under fluorescent light and got greenish pictures.
Underwater pictures might assume a bluish tint. If you do have
multiple images, select a representative one and use either the
Variations or the Curves dialogs to correct it. When the
correction is complete, save the curve or variation by clicking on the
Save button in the dialog. When you load the next picture, go to
the Variations or Curves dialog and click the load button, then select
the Variation or Curve you just saved. This will be applied to the
image. You can then further tweek the image using the dialog and
save the image with the corrections.
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Adobe Photoshop uses layers in the images. Normally, you think of an
image as a flat, one-dimensional object. However, in Photoshop you can
create multi-layered images. Think of an image with a number of
transparencies laid over it. These layers can be added, subtracted, or
blended with the other layers. Their order can be specified, they can be
edited individually, and they can be hidden. For instance, you can record
information about the image (who took it, where, when, what it is of, etc.) and
save this as a separate, hidden layer.
Normally, when you scan or open a scanned image, the picture is placed into a
layer called the background. Additional layers can be added with text or
arrows or whatever. Now, if you goof up one of these layers, or if you
want to move the position of an arrow, it is simple to do as long as it is a
separate layer and not part of the background. That's why you want to work
One big disadvantage of layers - they can only be retained in a few file
formats such as Photoshop (.PSD) files. A layered image cannot be saved as
a JPEG (.JPG), for instance. This is bad, because to open a PSD file you
need a fancier program, such as Photoshop, while any web browser can open a JPG
file. Also, layered files are much larger.
The moral: Work with layers until the image is just the way you want
it. The save it as a JPEG file, and, if you anticipate needing to edit it
again, save it as a PSD file as well.
Some tricks with layers:
|1. The Layers Pallette
||The Layers Pallette is usually on the right side of the screen (you
may have to click on its tab to bring it to the front). In the
figure to the right, you can see an image opened with 3 layers.
Layer 1 (red arrow) is visible (the eyeball tells you that) and is being
edited (that's the paintbrush and the blue highlighting). All it
contains is the red arrow (seen in the image of the fly). This
arrow could be moved or erased using the tools in the toolbox without
altering any of the background. The next layer is titled after its
text "Syrphid Fly". It is visible but it is not being
edited. If you look very closely at the rectangle next to the text
Syrphid Fly (move to the right from the blue arrow), you can just barely
see a squiggle of red in the lower left hand corner - this represents
the text in the image. Finally, the background level has the
actual picture in it, as you can see from the thumbnail there.
||You can right-click on a layer for several options which
include deleting or duplicating a layer. You can duplicate layers
from one image to another image as long as both images are open.
This is a quick way to put the same text (say "Copyright
2000") onto multiple images without retyping. You can also apply
various effects. There are also options available under the layers
menu. You can also adjust the transparency of a level by clicking
on the opacity button at the top right of the dialog; this allows you to
fade a layer in or out. You can rearrange the order of a layer by
using the Layer:Arrange menu; this gives you a choice of moving
the layer forward, backward all the way to the front, or all the way to
||Note: You cannot save a layered image as a JPG or
GIF (these options won't show up on the Save:File dialog). Before
you save the image you must either flatten the image (Layer:Flatten
Image) or use the File:Save For Web menu item. If you
choose the former, layers will be combined and the background
information under them will be overwritten (in other words, the change
is irreversible). If you choose the latter, it will create a new
file (JPG or GIF) which will be saved, then you can save the original
file as a PSD file and retain the layer information for later
editing. See the Saving Files section
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understand layers, then adding text is easy. The basic dialog is simple
enough. You can select the font, its style, its size, its color and its
orientation. Anti-Alias helps prevent slanted and round edges from looking
jagged. Kerning has to do with the width between letters; I forget about
leading, tracking and baseline. You can highlight any part of the text and
change its formatting, for instance you can make a single word bold. To my
knowledge there is no easy way to subscript or superscript; my workaround is to
add the superscript or subscript as a separate layer and move it into
position. Once there, they layers can be flattened or grouped so that they
will move together. As you type, the text will appear in the image
itself. You can highlight the text and make changes until you close the
dialog; once you close the dialog, you cannot easily edit the text; instead you
must delete the layer and start over.
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Often, you will need to select part of your image that is not a rectangle or
other geometric shape. For instance, you might have a picture of a
bird that you want to cut out to separate from its background so that you
can add it to an image showing a number of different birds (Note: In
scientific imaging, this is permissible only if it is obvious to the reader that
the image has been altered and that no distortion of reality occurs. I.E. it is
permissible to cut a bird out from its background; it is not permissible to then
add the bird to a different scene).
As usual, there are several ways to make a selection. I will show 3 of
these in detail here.
Selections via the magnetic lasso:
Selecting using the Magic Wand:
|1. Select the Magic Wand Tool.
|2. Set the Magic Wand Options.
||The main option to set is the Tolerance. When you
click with the Magic Wand, it selects the pixel under the cursor as well
as any adjacent pixels which have the same level or are within the
Tolerance setting of it. A bigger Tolerance Setting will allow the
Magic Wand to select more with each click, but it increases the chance
of selecting too much.
|3. Start Clicking.
||Click with the left button in an area you want to select.
|In most cases, a single click won't do it. Add to the
selection by holding down the SHIFT key as you click.|
|Remove areas from the selection by holding down the ALT key as you
|Sometimes it is easier to select the surroundings of an object and
|The image to the right shows the selection process in progress.|
|When you have completed the selection, proceed as you did above
after making a selection with the Magnetic Lasso.||
Using Quick Mask
|1. Make an initial selection using the Magic Wand (above)
|2. Toggle on Quick Mask.
|3. Expand the selection.
||When you toggle into Quick Mask, the area you selected will be
highlighted in red (or another color). Use any of the painting
tools to draw over the other areas you want to select (near right
image). When you are finished, the image should have red over
everything you want to select (far right image).
|4. Toggle back to regular viewing.
clicking on the icon to the left of the Quick Mask Icon, you will jump
back to regular viewing, and the masked area will become a selection.
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|The Magic Eraser can also be used to remove a background. It
works similar to the Magic Wand, but instead of selecting an area it
erases it, leaving a transparent background (or allowing a deeper level
to show through). Of course, you could also use the standard
eraser. If you don't see the Magic Eraser on the toolbox, click on
the eraser icon and hold for your options.
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Filters in Photoshop refer to effects that can be applied to the whole image,
or a selected part of it. Some of these filters recreate the effects that
filters mounted on camera lenses create. In scientific imaging, you will
probably keep the use of filters to a minimum. Two filters in particular,
sharpen and blur, are useful.
To sharpen or blur a selection:
- Select the area to apply the filter to.
- Go to the Filter menu and choose either the Sharpen or Blur submenu.
- From the choices, select the filter you want to use.
- If the effect is not enough, going back to the Filter menu will show that
the filter you just used is at the top of the list.
- Once you go to far with a filter, you can back up one step with the
Typically, it is necessary to use the sharpen filter 1-3 times on a scanned
image. Watch for noise (grain) to appear in the image, particularly in
areas without detail such as blue sky. This is a sign that you have gone
too far. Blurring of background can make a subject stand out even more, or
can blend away too much sharpness in a given area.
There are dozens of filters available in Photoshop, and more can be
purchased. Some representative examples can be viewed by following
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Aside from adding text, it is difficult to annotate figures in
Photoshop. Unlike full-featured drawing tools such as Corel Draw, the
tools available in Photoshop are limited, at least for those of us with little
artistic ability. For the artist, the sky is the limit as a number of
brushes and other tools are available to edit the image literally
bit-by-bit. Still, it is possible for even an amateur to add lines
and simple shapes. For more complex drawings, the companion program Adobe
Image Ready can be accessed from Photoshop.
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A number of other tools on the toolbox are useful for touching up areas of
the image. To blur out a small imperfection try the Smudge
tool. To sharpen a small area use the Sharpen tool; to blur it try
the Blur tool. Darken an area using the Burn tool, lighten
it using the Dodge tool. All of these tools can be reached from the
two icons shown above (the Smudge and the Dodge tool). If you click and
hold on the Smudge tool, you will be able to choose the Sharpen or Blur tools;
the Dodge tool will give way to the Burn tool. The Eraser Tool and the
Pencil Tool, mentioned earlier, can also be used to make small changes.
Sometimes it is helpful to use the View:Zoom In menu to examine the area
you are editing more closely.
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know how to correct a mistake you just made with the Edit:Undo menu. But
what if you don't notice a mistake immediately? Fortunately, you can go
back several steps using the History Tab at the right side of the screen. Simply
scroll back through the list to the command before your mistake and click
it. All of the intervening commands will be undone. Icons at the
bottom let you save a current state as a separate image.
|Be careful - only a given number of steps can be undone.|
|With some tools, such as the paintbrush or eraser, every click adds a line
to the history. This means you can run out of undo levels
|If you can't fix the problem by undoing, you can close the file without
saving it - then reopen it. Unfortunately, you lose all your
edits this way.|
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Most files can be saved simply by using the File:Save As menu.
Using Save As brings up a dialog allowing you to determine what type of file to
save it as. This table of file types might help:
Notes on Saving Images:
- If you are creating JPEG's, GIF's or BMP's, you must flatten the image
before saving it (Layer:Flatten Image).
- An alternate method of saving GIF's and JPG's is to use the File:Save
for Web menu. This brings up a dialog which gives you a great deal
of control over how your image is saved.
- If you want to make a GIF with a transparent background:
|Select the areas you want to be transparent.|
|Use the Help:Export Transparent Image menu to lead you through
the steps to making a transparent GIF.|
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These instructions are for the HP 7350 and
should also work for the HP 1115. Many of the comments are general enough
to fit other printers as well.
In Photoshop there are a few key printing
controls. The first consideration is the linkage between resolution and
image size. We measure resolution in pixels or dots per inch (from here on
out abbreviated DPI). All things being equal the more DPI the greater the
resolution. Since an image has a limited number of pixels, changing the
resolution will also change
the image size - unless resampling is checked. For printing, the
resolution should be between 200 and 300 DPI. If you make the change in
resolution with the resample image box checked (see image at right), then
Photoshop will adjust the image by interpolating (adding pixels) or simply
dropping pixels from the image as needed to make sure the image stays the same
size at the new resolution. This can adversely affect image quality.
On the other hand, leaving the box unchecked (as shown) will cause the image
width and length to change as you change resolution. If possible, change
resolution for printing with the resample box off; only turn it on if you cannot
get a useable image size with a resolution between 200 and 300 DPI.
The Page:Setup dialog opens up the other key
surface, this is a simple dialog:
At the least, make sure you are printing to
the correct printer, and that the paper choices are correct in terms of size and
orientation. Most of the real work is hidden behind the PROPERTIES
For photos you should select best (unless
this is a trial run, and you should try to avoid those), and select the correct
Paper Type. Failure to select the correct paper type can lead to ink
spillage and streaks on your paper. There is also a button (on the HP 7350
at least) for HP Digital Photography settings.
I usually leave these all turned off.
Under the layout tab are other options.
Again, be sure the paper size and orientation are correct (you can set this in
several places and the software does not always communicate your choices).
Leave the scale to fit unchecked (Photoshop is handling that), and be sure you
are printing only one copy. It's not a bad idea to click the Factory
Settings buttons now and then to be sure someone else hasn't made drastic
With all settings confirmed, OK your way out
of the dialogs and print.
There is more on printing here:
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