High Quality Images

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How to capture high quality images for publication

The method used to capture high quality images can vary depending on the web browser and the operating system you use. Here is what we do:

Save the displayed web page to a high resolution PDF file
Convert a PDF file to an image file, use image editor to edit the image you want

We will introduce a list of file conversion and image editor applications we use in the following paragraphs.

Save a web page to a PDF file

For Next Generation Clustered Heat Maps (NG-CHM) user

Go to the top of the web page, click Misc -> PDF, save the generated PDF to your local hard disk.

For other software applications user

Chrome

Chrome (e.g. version 36.0) will capture high quality images on either Mac (version 10.8.5 and above) or Windows (version 8 and above).

After opening the web page in Chrome, follow these steps:

Open menu, choose Print, the print setting dialog pops up
Destination: click Change, choose Save as PDF, save to your local hard drive

Please refer to Google’s Chrome Support link: https://support.google.com/chrome/answer/1379552?hl=en

Safari

Safari (e.g. version 6.0.5) will capture high quality images on a Mac (e.g. version 10.8.5).

After opening the web page in Safari, do

File->Print, click PDF, Select Save as PDF on your local hard drive.

Firefox

For Linux user, after opening the web page in Firefox (e.g. Version 24.6), do

File->Print->Adobe PDF, save to your local hard drive

On Windows and Mac, Firefox (e.g. Version 31.0) has the Adobe Acrobat PDF plugin automatically installed. We found this combination failed to capture high resolution of the graphics which are generated in our web pages. If you save a web page using Adobe Acrobat PDF plugin, it generates a low resolution PDF file that can’t be used to convert to an image file for publication purpose. This is not recommended for Windows and Mac user.

Convert a PDF file to an image file

You can use various file conversion applications(e.g. Adobe Acrobat Pro, Preview, GIMP) to convert a PDF file to other image formats (e.g. PNG, TIFF, etc.). Different conversion applications will have different methods to save images into a new format. For example:

If you open the PDF file in Adobe Acrobat Pro, do File -> Save As Other -> Image -> PNG
If you open the PDF file in Preview, do File -> Export->Format->PNG
If you open the PDF file in GNU Image Manipulation Program (GIMP), do
- File->open, select your PDF file, a dialog box pops up
- Import As, choose Resolution: e.g. 300 pixel/in (or above, based on the quality you desire)
- go to Image-> Set Image Print Resolution, choose x resolution and y resolution 300 pixel/in (or above, based on the quality you desire)
- File->Export, select File Type (By Extension) as png, tiff etc
Use ImageMagick

ImageMagick command line tool convert can convert a PDF file to an image file. You can use the density option to obtain a high quality image. For example:

convert -density 300 my.pdf my.png

Please refer to ImageMagick to install ImageMagic for Windows and Linux. Be aware of installing Ghostscript before using ImageMagick PDF file conversion.

Note:

For Linux user, If you open the PDF file in Adobe Reader, for example Adobe Reader9, do

Tools -> Select & Zoom -> Snapshot Tool

Paste to an image editor, the image quality might be all right. However,

For Windows and Mac, Adobe Reader does not have Save As Other->Image option. From our experience, to process with Adobe Reader, Edit- > Take a Snapshot, the images are in low resolution. So we do not recommend Adobe Reader as a conversion tool for Mac and Windows.

Edit an image file

There are many image editors such as GIMP, Adobe Photoshop and Paint that allow you to crop or annotate the image.

Department of Bioinformatics and Computational Biology

How to capture high quality images for publication

Save a web page to a PDF file

Convert a PDF file to an image file

Edit an image file