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 figures 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'
ProblemPublication 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'
ProblemPublication 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'
ProblemPublication 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' ProblemDigital
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' ProblemDigital
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' ProblemDigital
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' ProblemDigital
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' ProblemDigital
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 Adobes 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' ProblemGeneral
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' ProblemGeneral
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' ProblemGeneral
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 images number of total pixels is
  fixed when 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' ProblemGeneral
Guidelines

• Visual example of creating new pixels.

16
Handling the 'What Comes First' ProblemGeneral
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' ProblemGeneral
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.
  
• Dont 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 2 Use 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 doesnt 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 youll 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 dont need.

23
Resources

• Software Toolbox
• Photo-editing Software
• Adobe Photoshop - http//www.adobe.com/products/ph
  otoshop/
• Corel Paint Shop Pro - http//www.corel.com/paints
  hop/
• Microsoft PhotoEditor - http//office.microsoft.co
  m
• Line-art Software
• Adobe Illustrator - http//www.adobe.com/products/
  illustrator/
• ACD Systems Canvas - http//www.acdamerica.com/pro
  ducts-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/Pri
  sm.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/in
  design/
• Adobe PageMaker - http//www.adobe.com/products/pa
  gemaker/
• Quark Express - http//www.quark.com/products/xpre
  ss/

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.