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Digital Filters

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 Grids Cropping and Sizing Images Adjusting Brightness and Contrast Adjusting Color
Layers Adding Text Using the Magic Eraser Making Selections
Using Filters Smudging

Adding Lines and Figures

Undoing Mistakes with the History Tab

Saving Files



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.

Flatbed Scanners Nikon LS-2000 Overview

Nikon LS-2000 Details


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 item.
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 and Sizing Images

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 size dialog.

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 automatically. 
 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 pixels/inch
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 several images.

To adjust the Canvas Size:

  1. Set the background color to the color you want the added canvas to be.
  2. Use the Image:Canvas Size menu to open the Canvas Size dialog. 
  3. Set the width and the height that you want it.
  4. 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.
  5. Click OK.


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Adjusting Brightness and Contrast

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.

Method 4.


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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Adjusting Color

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.


  Pixel Values
Color on Screen Red Green Blue
Red 255 0 0
Green 0 255 0
Blue 0 0 255
Black 0 0 0
White 255 255 255
Yellow 210 254 1


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.

Incidentally, there are several ways to select a color to draw lines or add text with in Photoshop.  
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 picker.
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.


Method 1.

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.
Method 3.

Adjust Curves

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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Using Layers

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 with layers.

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 the back.
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 for instructions.

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Adding Text

If you 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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Making Selections

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:

1. Choose the magnetic lasso tool. Select the Magnetic Lasso tool from the toolbox. (if the magnetic toolbox is not the current selection, click and hold on the lasso icon to see the other selections.  The Magnetic Lasso has the magnet on it.
2.  Set the parameters for the lasso. The 3 most important settings are the Lasso Width, the Frequency, and the Edge Contrast.  The Lasso Width determines the size of the cursor.  The Magnetic Lasso tries to find an edge in the area under the cursor; a larger setting will make for quicker drawing but may not give you a close selection.  The frequency refers to the number of points used (per inch) for making the selection.  The Edge Contrast adjusts the sensitivity; a smaller number is more sensitive but slower.
3.  Draw around the object. Simply click on the edge and work your way around the object.  The selection line will stick to the edges of the object.
If you mess up, hit the delete key to remove the last few points on the selection line.
If the program can't find the edge; you can manually set a few points by clicking the left button.
When you are back near the selection point click enter to complete the loop (left picture).
With the object selected, use the Select:Inverse menu item to select everything BUT the object (right picture).
4.  Delete the background. Hit the delete key or use Edit:Cut from the menu.  The image will look like the image to the right.  
If you want to make the background transparent, use the Help:Export Transparent Image meni item BEFORE deselecting.
You can then use the Select:Deselect menu to remove the dashed lines.
You can use the Select:Inverse menu to revert to a selection of the object, which can then be Edit:Copied and Edit:Pasted into another image.
 These two images have been prepared and saved differently, the image on the left was saved with a white background; the image on the left has a transparent background.  Note how the transparent background allows the grid of the web page to show through right up to the bird.

 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 click.
Sometimes it is easier to select the surroundings of an object and use Select:Inverse.
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. By 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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Using the Magic Eraser


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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Using Filters

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:

  1. Select the area to apply the filter to.
  2. Go to the Filter menu and choose either the Sharpen or Blur submenu.
  3. From the choices, select the filter you want to use.
  4. 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.
  5. Once you go to far with a filter, you can back up one step with the Edit:Undo menu.

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 this link.

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Adding Lines and Figures

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.

1.  Adding a line or arrow. Use the line tool (it may show up on the toolbox as a pencil; click and hold the pencil tool to change to the line tool).  The options are simple; you can set the weight (thickness) of the line and whether it will have an arrowhead at its start, its finish or both.  You can also change the shape of the arrowhead.
2. Drawing a circle or rectangle. This is tricky.  There is no easy way to do it in Photoshop; you could jump to ImageReady, but I have a little trick:
Add a new layer (Layer:New:Layer menu)
In that layer, use the rectangular or circular marquee to create a rectangle or circle in the place where you want it.
Use the Select:Modify:Border menu.  The width will be the width of the line you will draw.
Use the Paintbucket tool to fill the selection.
Flatten and save the image.
3. Use ImageReady

The Adobe ImageReady program has a different toolbox and may be more suited to what you are trying to do.  It can be opened by clicking on its icon at the bottom right of the toolbox.

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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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Undoing Mistakes with the History Tab

You already 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 fast.  
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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Saving Files

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:

File Type

Relative Size Features Disadvantages
Adobe Photoshop (.PSD) Huge
Retains Layers and other Photoshop extensions
Highest image quality
Must edit in Photoshop
Must view in Photoshop
JPEG (.JPG) Small
Retains much color information
Variable compression ratios
Can be used on web pages
Can be viewed with web browsers (Netscape)
Can be edited with many programs


Lower image quality
No layers
GIF (.GIF) Small
Can be used on web pages
Can be viewed with web browsers (Netscape)
Can be transparent
Can be interlaced
Can be animated
Can be edited with many programs
Good for drawings


Only 256 Colors
Lower image Quality
No layers


Can be used as Windows Wallpaper
Can be edited by many, many  programs
Good image quality
Large size
No layers

Notes on Saving Images:

  1. If you are creating JPEG's, GIF's or BMP's, you must flatten the image before saving it (Layer:Flatten Image).
  2. 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.
  3. 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 printing controls. On the 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 button...









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 changes.


With all settings confirmed, OK your way out of the dialogs and print.






There is more on printing here:

Digital Filters

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