Dr. Mom, My Adventures as a Mommy-Scientist

Discussion of my journey from grad school to postdoc to tenure with two kids, a husband, (and a bit of breast cancer) in tow.

Monday, November 21, 2005

Writing your first paper: Step Six: Results-Figures

Well, I'd like to thank everyone for their patience in this series. I am finally back to normal after getting my 71 page bookchapter out the door (and only two weeks late!) So now I'd like to resume my discussion of writing a research paper.

In the results section, figures are the most important part. These are the components most likely to be glanced at by a reader interested in your work. Each advisor has his/her own theory for how figures should be formatted, so the guidelines below are just that: guidelines, but should give you one option for creating professional-looking figures, without writing nastygrams to Bill Gates along the way.

Preparing (and Compressing) Images in Adobe
Images are probably the easiest figures to prepare. You snap the image with your camera, microscope, SEM, TEM (whatever) and voila! To insert an image into your test you can add it directly using the insert picture function in word, but I wouldn't recommend this. I usually adjust my figures first using Adobe photoshop. You can get some great student discounts on this product and it is definitely worth it. I use adobe to size and compress figures. This prevents my word document from becoming a behemoth (and also likely to crash). Print resolution is usually 300 dpi and screen resolution only 72 dpi so you don't need much. To adjust a figure in adobe, first open the image. Use the image-adjustments-brightness/contrast feature to get a good image. Then, use the rectangle tool to crop out unnecessary portions of the image. Next, use the image-image size function to reduce the image to the dpi and size you need for your paper (usually width maximum of 6 inches and 300-600 dpi). Now you can save your image as a JPEG and compress as needed to fit in your document. I usually compress to 6 (medium).

To create a composite image, first adjust each individual image. Then, create a new image (file-new) with the appropriate height and width requirements. Paste the two individual images into the new image and save as JPEG. If you mess up positioning you can use the history function. This shows all the changes that you have made to a document and by simply clicking on a change you can undo all those changes made after it.

Adding scale bars and text to images in Word
An important thing to remember about images is the scale bar. For TEM or SEM a scale bar is usually printed directly on the image. Because these are typically hard to read and small, I crop these out and make large (i.e., thicker, darker) scale bars of the same size. In the case of microscopic images, you can use a hemocytometer (cell counter) to determine scale bars. The dimensions of a hemocytometer are known (see the product insert). You can measure the distance between squares using the measure function in Adobe (right click the eyedropper in the tool bar to get the ruler). Then, you can set-up a proportion to determine the needed scale bar. For example, if a 200 micron square of the hemocytometer is 2.5 cm on your image, you can make a 50 micron scale bar that is 0.625 cm long.

I tend to draw scale bars on images that I have pasted into a separate word document (different from the actual paper so that if it crashes I only lose that one image). Adobe is notoriously poor at transferring text so I usually put all text (scale bar caption, figure numbering) in using word as well. This can be difficult. For best results, convert the image to behind text (right click image, format, layout). Then, write your text using text boxes (drawing toolbar) but DO NOT write in the "provided drawing space." Move your text over the image. Select the image using the drawing pointer. From the drawing toolbar select send to back, then group the image and the text together. Select the picture again, this time using the text (not drawing tools, unclick the arrow), and format the image layout to inline with text.

Figure Captions
Once you have the figure you just have to prepare a simple caption. Try to make as concise as possible. First line should be a phrase saying what the image is, with subsequent sentences providing detail. For example:

Figure 1: Visual Comparison of Ice Cream Textures. Ice cream texture of (A) liquid nitrogen, (B) hand-crank, and (C) electronic machine made ice-cream. Notice the lack of ice crystals (arrows) in the liquid nitrogen and hand crank preparations.

This caption combines all the A,B,C labeling into one sentence. Where possible this is preferred. Then it makes a small comment on the image. Save the big stuff for the discussion section. Remember that results is results only, not interpretation.

Charts and Graphs
Oh the beauty of excel! (or lack thereof). Because this is what most people use I will confine my discussions to this program. If you are a lucky owner of Kalediagraph or similar program, just go enjoy your program and leave the rest of us to suffer through the wrath of microsoft.

Formatting Graphs and Charts in Excel
Graphs and charts should have a white background with black text. If possible, charts should be black and white only to limit color image costs. Ideally, the graph/chart would not contain a legend, with each line labeled directly by a text box. This can be done using the drawing functions in excel and is straightforward, just remember to group the text to the graph before pasting. If space is limited and direct labeling is not possible, use dashed lines or different shapes as symbols to label the lines. If colors are imperative, it is better to use blue, red, green, yellow in that order (easier to see, more professional, and personal preference, you may disagree).

In the case of overlapping comparisons of multiple lines (e.g., comparing FTIR spectra, UV-VIS) it is helpful to offset each of the data lines. However, for this to work, the axis must be arbitrary (as is the case for most spectroscopy). To do this, you can simply multiple each data point by 50%, 75%, or 100% (etc.) to create a graph with the same x-axis, but arbitrary y.

If a particular point is hard to see, but enlarging the entire graph is a space-waster, consider using an insert. You can make a copy of the graph in question, scale the axes to display only the point of interest, and then use Adobe to paste the 'inset' into the main image. Save the composite as a JPEG and paste into your document.

In general, graphs should not contain a title (it is included in the figure caption) or general border. They should contain a chart border, x and y axis labels (even if the y axis is arbitrary units), and labels for each data set.

Pasting a Graph from Excel into Word
Oh how many times have I crashed my program here! The key is to not control-c, control-v (i.e., paste directly). This creates an excel graph that may be edited from the word document and is linked to any changes in the excel document. While this sounds great in theory, it takes up SOOO much space and memory. Instead, paste as an enhanced metafile and your life will be much, much easier.

Drawing your own images in powerpoint
Drawing your own images is easy. I usually use powerpoint for this, but you could use a separate word doc as well. They key to creating your own professional looking images is two fold. First, use the group and paste commands to create repetitive sequences rather than drawing each one. For example, I once had the please of drawing a plasma membrane lipid by lipid. I simply drew a couple of lipids on either side of the bilayer and then grouped them. They can then be copied and pasted to create a membrane of any length. Second tip, use the fill effects function to create more professional colorations. One I like is to use the gradient function (play around with it, its pretty neat) when creating a background for an image (e.g., the cytosol behind my plasma membrane). This is especially useful when you are only drawing part of something and want to give the impression that it continues off into space.

If things don't line up correctly or you are having drawing what you want, make sure that drawing toolbar-grid-snap objects to grid, snap objects to objects, is unchecked. Also, you can blow up the whole image to 200-400 to get a handle on small portions of the image. Before pasting, adjust the figure to its intended size, making sure that text is readable. As with excel, paste images over as an enhanced metafile if you don't want a major headache.

Well, I know this discussion was highly technical, but I hope it saves a few people the horror that was the writing of my dissertation.


At 4:11 AM , Blogger twf said...

You use MS Office products for scientific papers? Wow. I once handed in a paper written in Word for a class I took from my thesis advisor. She told me I was NEVER to give her anything written in Word again. Everything is LaTeX. Figures are made using xfig.

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