Difference between revisions of "Converting microarray images"
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=Imagemagick= | =Imagemagick= | ||
| − | Once installed, all image magick tools are accessed through the command line. The ''[http://www.imagemagick.org/script/identify.php identify]'' binary describes the format and characteristics of one or more image files. | + | Once installed, all image magick tools are accessed through the command line. The ''[http://www.imagemagick.org/script/identify.php identify]'' binary describes the format and characteristics of one or more image files. e.g. |
| + | <table class=document-code><tr><td> | ||
| + | identify rose.jpg | ||
| + | rose.jpg JPEG 640x480 DirectClass 87kb 0.050u 0:01 | ||
| + | </table> | ||
| + | |||
The ''[http://www.imagemagick.org/script/convert.php convert]'' binary is useful for resizing images, for example; | The ''[http://www.imagemagick.org/script/convert.php convert]'' binary is useful for resizing images, for example; | ||
<table class=document-code><tr><td> | <table class=document-code><tr><td> | ||
Revision as of 23:11, 10 September 2006
Microarray images are generally stored as 16-bit TIFF images (usually around 100Mb in size. An alternative lossy image format is JPEG format, which is still bloated at around 40Mb filesize. Investigating the image size of a typical GenePix derived JPEG image, the pixel size is 4400 × 14300 pixels (72 pixels per inch) with an aspect ratio of 3.25 . A general visual summary of these lossy images is all that is required where they could be converted to a much smaller thumbnail PNG type image using an appropriate program such as ImageMagick or Gimp which allows batch processing of multiple images a once.
Imagemagick
Once installed, all image magick tools are accessed through the command line. The identify binary describes the format and characteristics of one or more image files. e.g.
identify rose.jpg rose.jpg JPEG 640x480 DirectClass 87kb 0.050u 0:01 |
The convert binary is useful for resizing images, for example;
|
convert -size 800x600 input.jpg'[80x60]' output.png |
will resize and convert a JPEG to a PNG. The mogrify binary will convert an entire directory of images; mogrify -format jpg -size 800x600 *.jpg
