What Comes First?

1. 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

2. 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.

3. 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.

4. 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

5. 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!

6. 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

7. 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)

8. 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.

9. 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

10. 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.

11. 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.

12. 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

13. 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.

14. 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.

15. Handling the 'What Comes First' Problem:General Guidelines • Visual example of ‘creating new pixels’.

16. 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.

17. 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.

18. 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

19. 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.

20. 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).

21. 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

22. 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.

23. 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

24. 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/

25. 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/

26. 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.