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What Comes First? Preparing Digital Images for Publication Suzanne Paquette, J Histochem Cytochem Histochemistry 2006: The Nexus of Histochemistry and Molecular Genetics August 23-27, 2006 Hilton Waikoloa Village, The Big Island of Hawai'i, USA

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What comes first l.jpg

What Comes First?

Preparing Digital Images for Publication

Suzanne Paquette, J Histochem Cytochem

Histochemistry 2006: The Nexus of Histochemistry and Molecular Genetics

August 23-27, 2006

Hilton Waikoloa Village, The Big Island of Hawai'i, USA


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What Comes First: the Figures or the Manuscript?

  • Until your paper is written, you may not know:

    • Which data and images will become figures

    • How you will present or arrange the figures

  • Not all figures can be treated the same.

    • Different figure types have different publishing requirements.

    • Image file types and software drastically effect figure handling.

  • This can create a ‘what comes first?’ problem

    • Potential figure data may exist before the manuscript itself.

    • The Result: You must be thinking about publication requirements when you generate any potential figure data.


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Handling the 'What Comes First' Problem

  • Know the difference between publishing industry and digital imaging terms.

    • Publishers are concerned with a figure’s content.

      • Does the figure have graphs, diagrams, or photographs?

      • Is the figure in color?

    • Digital Imaging is concerned with file type and software.

      • Can the file only be opened by a specific program (proprietary)?

      • Is it a pixel-based image or a line-art image?

  • Follow general guidelines for figure publication

    • There are trends in image requirements you can follow.

    • You are more likely to make a figure that a publisher can use if you follow these trends.


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Handling the 'What Comes First' Problem:Publication Industry Terms and Definitions

  • Terms and Definitions – Publication Industry

    • Continuous-tone Figures: figures made of photographic content, with labeling on the image.

    • Visual Examples. No external labeling!

      Images courtesy of Dr. Richard W. Burry


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Handling the 'What Comes First' Problem:Publication Industry Terms and Definitions

  • Line-art Figures: figures that are line-drawings, graphs, diagrams, or text and that contain no continuous-tone figures.

  • Visual Examples. No photographic images!


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Handling the 'What Comes First' Problem:Publication Industry Terms and Definitions

  • Combination Figures: a combination of line-art figures, continuous-tone figures, and/or external text labeling.

  • Visual Examples

    Images courtesy of Dr. Richard W. Burry


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Handling the 'What Comes First' Problem:Digital Imaging Terms and Definitions

  • Terms and Definitions – Digital Imaging

    • Resolution: a measure of the number of pixels (dots) in a unit of distance on the image. Common measurements: dots per inch (DPI) and pixels per centimeter (PPC)


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Handling the 'What Comes First' Problem:Digital Imaging Terms and Definitions

  • Rasterized Image Files: image files made of pixels or dots. Types of rasterized image file include TIFF, Bitmap, JPG, and GIF.

  • Line-art Image Files: image files defined as a series of lines, vectors, objects, and blocks of text. Types of line-art image file include EPS, PDF, and Metafile.

  • These terms are not based on the content of the image, they are based on the digital format of the image file.

    • A specific image file format is not limited to a certain type of image content.

    • The content of a given image file could be a continuous-tone image, a line-art image, or a combination image.


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Handling the 'What Comes First' Problem:Digital Imaging Terms and Definitions

  • An example of a line-art figure (a chemical diagram) saved as a Rasterized Image File, and as a Line-art Image File.

Rasterized Image File

Line-art Image File


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Handling the 'What Comes First' Problem:Digital Imaging Terms and Definitions

  • Rasterize/Rasterizing: converting a Line-art image file into a Rasterized Image file.

    • Usually done by opening the Line-art image file in a photo-editing program (eg. Adobe Photoshop, Jasc Paint Shop Prot).

    • ‘Rasterizing’ a line-art image file produces a copy of it with a fixed resolution and size.

    • This new copy is made of pixels, thus it is a Rasterized Image File.


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Handling the 'What Comes First' Problem:Digital Imaging Terms and Definitions

  • Proprietary File Format: a file format that requires a specific program or version of a program to be opened.

    • PSD (Adobe Photoshop) and PPT (Microsoft Powerpoint) are examples of proprietary file formats.

    • Because of this limitation, most publishers will ask for non-proprietary formats, which include TIFF, BMP, EPS, and JPG.

    • Special Case: Adobe’s PDF format is not strictly a proprietary format, because programs other than Adobe software can open and in some cases even edit a PDF. Many publishers will allow you to submit a figure in PDF format, however you must check with your publisher first.


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Handling the 'What Comes First' Problem:General Guidelines

  • General Guidelines

    • Always keep basic image requirements for review and publication in mind

    • Always capture or scan image at the highest resolution possible.

    • Keep copies of your original, unedited, source files.

    • Use the appropriate file-types and formats


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Handling the 'What Comes First' Problem:General Guidelines

  • Basic Image Requirements for Review and Publication

    • High resolution (300-900 DPI) must be present when the figure is generated, and cannot be created later. Resolution requirements vary from 300 DPI to 900 DPI depending on the image content.

    • Non-proprietary file types (TIFF, EPS, JPG, etc.) do not require specific programs or versions to be opened or edited, ensuring that your publisher can use your files.

    • Standard fonts (Arial, Times or Times New Roman) should be used for any labeling – your publisher may not have copies of other fonts, and substitutions can introduce errors in your figures.


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Handling the 'What Comes First' Problem:General Guidelines

  • Generate Images at High Resolution

    • Images must be generated in high resolution, because it cannot be added later. This includes:

      • When an image is captured (eg. with a camera, microscope)

      • When a photograph, printout, or slide is scanned with a scanner

      • When a drawing is made in a photo-editing program

      • When a line-art image is exported as a rasterized image (TIFF, Bitmap, or JPG).

    • A rasterized image’s number of total pixels is fixedwhen it is generated.

    • This means the resolution at a given size is also fixed.

    • Attempting to raise the resolution can result in a loss of sharpness and distortions in the image as your photo-editing software generates new pixel data.


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Handling the 'What Comes First' Problem:General Guidelines

  • Visual example of ‘creating new pixels’.


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Handling the 'What Comes First' Problem:General Guidelines

  • Keep Unaltered Copies of Your Source Files

    • All image data should be kept in some unlabeled, uncropped, and unsized format.

    • There is always the possibility that:

      • You will decide to rework a figure.

      • The publisher will request substantial changes.

      • You will notice an error that must be corrected.

    • If your original source image and data files are available to you, correcting or re-creating your figures is much easier.


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Handling the 'What Comes First' Problem:General Guidelines

  • Use Appropriate File Types

    • Only some programs are ideal for specific image types.

    • Using them to create and edit other image types may not produce publishable results.

    • Continuous-tone Figures: Use rasterized image formats such as TIFF and BMP. Some publishers allow JPGs.

    • Line-art Figures: Use line-art image formats such as EPS, PS, PDF, EMF, and WMF.

    • Combination Figures: Line-art image formats can often accomodate the continuous-tone images in a combination image. Rasterized formats require a resolution of 800 DPI or more to support a combination, and are not preferred.


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Figure Preparation and Layout

  • Plan your figures before you start to create them.

    • Decide which images will make up each figure.

      • Isolating graphs and line-art from continuous-tone images (micrographs, photographs) can simplify figure creation.

      • Combining line-art and continuous-tone images can create sophisticated figures that convey a good deal of data.

    • Decide on the layout and labeling of each figure.

      • Don’t use your software - Make hand-drawn layouts in pen/pencil, or using photocopies of your images.

      • Saves time, is easily changed, and requires no computer skills


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Figure Assembly

  • Different figure types demand different assembly procedures.

    • Continuous-tone figures with labeling directly on the images should be assembled with photo-editing software.

    • Line-art figures are best handled in a line-art program. Graphs should be made in graphing software, then exported for use in a line-art program; diagrams and schematics should be drawn in line-art software and exported as an EPS or PDF file.


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Figure Assembly

  • Combination figures are best assembled using a combination of programs.

    • Generate/Edit the individual panels in the appropriate software.

      • Graphs: graphing software

      • Drawing, diagrams: line-art software

      • Continuous-tone images: generate at the highest resolution possible, edit using photo-editing software.

    • Combine the figure panels

      • Option #1 Use software that can handle both rasterized images and line-art, graphs, or diagrams: Microsoft Powerpoint; Adobe InDesign, PageMaker, or Illustrator; Canvas; Quark Express

      • Option #2Use photo-editing software to assemble your combination figure as a very high resolution TIFF or BMP image (minimum of 800 DPI).


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What Really Comes First?

  • Creating publishable figures doesn’t have to be difficult.

    • Some familiarity with the needs of publishers can allow you to anticipate their requests.

    • Following general guidelines for figure generation can smooth over the publication process, no matter who you publish with.

    • Planning your figures can save you time as well as frustration in working with imaging software.

  • The easier it is to make your figures, the more time and energy you’ll have for the rest of the manuscript


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Resources

  • How do I find out how to do something in these imaging programs?

    • Some programs have very useful Help sections.

      • Most software will have a Help option on the Main Menu.

      • Some programs have searchable Help files full of tips and tricks (this is especially true of Adobe software).

    • Google It!

      • Google lets you do a full-text search of the World Wide Web, thus enabling you to locate tips and tricks posted by others!

      • Learn how to search with keywords that will quickly locate helpful information, while skipping information you don’t need.


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Resources

  • Software Toolbox

    • Photo-editing Software

      • Adobe Photoshop - http://www.adobe.com/products/photoshop/

      • Corel Paint Shop Pro - http://www.corel.com/paintshop/

      • Microsoft PhotoEditor - http://office.microsoft.com

    • Line-art Software

      • Adobe Illustrator - http://www.adobe.com/products/illustrator/

      • ACD Systems Canvas - http://www.acdamerica.com/products-x/x/

      • CambridgeSoft ChemDraw and BioDraw - http://www.cambridgesoft.com/software/

    • Graphing Software

      • Microsoft Excel - http://office.microsoft.com

      • Systat SigmaPlot - http://www.systat.com/products/sigmaplot/

      • Graphpad Prism - http://www.graphpad.com/prism/Prism.htm


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Resources

  • Software, cont.

    • Publishing/Presentation Software –

      These programs are useful in combining complex images, such as combination figures, but in some cases require a good deal of practice to use efficiently.

      • Microsoft Powerpoint, Microsoft Publisher - http://office.microsoft.com

      • Adobe InDesign - http://www.adobe.com/products/indesign/

      • Adobe PageMaker - http://www.adobe.com/products/pagemaker/

      • Quark Express - http://www.quark.com/products/xpress/


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Resources

  • Workshop Syllabus and Presentations

    • Available on the Histochemical Society website in high- and low-resolution PDF formats.

    • Contains demonstrations and examples as well as this presentation in full-text format.

    • http://www.histochemicalsociety.org/presentations/


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Examples and Demonstrations

  • Sizing Your Newly Captured Images

    • Introducing the ‘Image Size’ window

    • Resolution and interpolating image data

  • Converting Powerpoint slides into TIFFs

    • Generate your Powerpoint slide

    • Generate an Adobe PDF using Acrobat Distiller

    • Rasterize the PDF in Photoshop at an appropriate resolution.


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