Talk:Converting microarray images

Hi Sven, was just wondering why you are converting tiff to jpeg? Jpeg is going to introduce a lot of artifacting and I imagine this would have a very bad affect on your results. If your source is TIFF consider using the LZW compression with binary encoding to save space and then translate this directly into PNG with imagemagick. In this way the only loss will be the pixel colour rounding error introduced with the conversion from 16bpp to 8bpp. This is still a lot of error though.

Check this: wikipedia:png. It looks like the PNG format supports 48bit colour spaces, so you could keep the whole 16bits per pixel in the conversion to PNG and not have to discard any data. --Rob 12:48, 14 Sep 2006 (NZST)

The problem is that the microarray images are proprietary 16-bit TIFF images of two channels plus a whole lot of auxillary information. If I use imagemagick to examing the filetype it think there are two images and converts them both to two separate PNG's (which is not what I want). I am forced to use the software that does the scanning of these images to convert to a lossy format first before making cut down PNG's. To reduce the loss I want JPG's that are as big in filesize as possible, we start with 110Mb TIFF's and convert to 40Mb JPEG's.

$ identify AT45.tif AT45.tif[0] TIFF 3760x8112+0+0 PseudoClass 65536c 16-bit 116.4m 1.1u 0:02 AT45.tif[1] TIFF 3760x8112+0+0 PseudoClass 65536c 16-bit 116.4m 0.5u 0:01

( --Sven 14:52, 14 Sep 2006 (NZST)

If imagemagick understands then it's sweet. Just grab your 2 channels and assign them to R and G and leave B and A blank. That way you have a RGBA compatible colour space. Save this out as a PNG. I haven't played with imagemagick but if it can deal with channels then it can construct as many as are needed. --Rob 16:47, 14 Sep 2006 (NZST)

Not sure exacty what you mean, what package would you normally do this in? Photoshop cannot understand these images. Here is the options in Imagemagick'sconvert binary;

$ convert Version: ImageMagick 5.5.1 10/15/02 Q16 http://www.imagemagick.org Copyright: Copyright (C) 2002 ImageMagick Studio LLC Usage: Magick [options ...] file [ [options ...] file ...] [options ...] file Where options include: -adjoin join images into a single multi-image file -affine matrix affine transform matrix -antialias remove pixel-aliasing -append append an image sequence -authenticate value decrypt image with this password -average average an image sequence -background color background color -blue-primary point chomaticity blue primary point -blur geometry blur the image -border geometry surround image with a border of color -bordercolor color border color -channel type extract a particular color channel from image <-------------------- -charcoal radius simulate a charcoal drawing -chop geometry remove pixels from the image interior -clip apply clipping path if the image has one -coalesce merge a sequence of images -colorize value colorize the image with the fill color -colors value preferred number of colors in the image -colorspace type alternate image colorspace -comment string annotate image with comment -compress type image compression tyhpe -contrast enhance or reduce the image contrast -crop geometry preferred size and location of the cropped image -cycle amount cycle the image colormap -debug events display copious debugging information -deconstruct break down an image sequence into constituent parts -delay value display the next image after pausing -density geometry horizontal and vertical density of the image -depth value image depth -despeckle reduce the speckles within an image -display server get image or font from this X server -dispose method Undefined, None, Background, Previous -dither apply Floyd/Steinberg error diffusion to image -draw string annotate the image with a graphic primitive -edge radius apply a filter to detect edges in the image -emboss radius emboss an image -encoding type text encoding type -endian type LSB or MSB -enhance apply a digital filter to enhance a noisy image -equalize perform histogram equalization to an image -fill color color to use when filling a graphic primitive -filter type use this filter when resizing an image -flatten flatten a sequence of images -flip flip image in the vertical direction -flop flop image in the horizontal direction -font name render text with this font -frame geometry surround image with an ornamental border -fuzz distance colors within this distance are considered equal -gamma value level of gamma correction -gaussian geometry gaussian blur an image -geometry geometry perferred size or location of the image -green-primary point chomaticity green primary point -gravity type horizontal and vertical text placement -help print program options -implode amount implode image pixels about the center -intent type Absolute, Perceptual, Relative, or Saturation -interlace type None, Line, Plane, or Partition -label name assign a label to an image -level value adjust the level of image contrast -limit type value Disk, Map, or Memory resource limit -list type Color, Delegate, Format, Magic, Module, or Type -loop iterations add Netscape loop extension to your GIF animation -map filename transform image colors to match this set of colors -mask filename set the image clip mask -matte store matte channel if the image has one -median radius apply a median filter to the image -modulate value vary the brightness, saturation, and hue -monochrome transform image to black and white -morph value morph an image sequence -mosaic create a mosaic from an image sequence -negate replace every pixel with its complementary color -noop do not apply options to image -noise radius add or reduce noise in an image -normalize transform image to span the full range of colors -opaque color change this color to the fill color -page geometry size and location of an image canvas -paint radius simulate an oil painting -ping efficiently determine image attributes -pointsize value font point size -preview type image preview type -profile filename add ICM or IPTC information profile to image -quality value JPEG/MIFF/PNG compression level -raise value lighten/darken image edges to create a 3-D effect -region geometry apply options to a portion of the image -raise value lighten/darken image edges to create a 3-D effect -red-primary point chomaticity red primary point -render render vector graphics -resize geometry resize the image -roll geometry roll an image vertically or horizontally -rotate degrees apply Paeth rotation to the image -sample geometry scale image with pixel sampling -sampling-factor geometry horizontal and vertical sampling factor -scale geometry scale the image -scene value image scene number -seed value pseudo-random number generator seed value -segment values segment an image -shade degrees shade the image using a distant light source -sharpen geometry sharpen the image -shave geometry shave pixels from the image edges -shear geometry slide one edge of the image along the X or Y axis -size geometry width and height of image -solarize threshold negate all pixels above the threshold level -spread amount displace image pixels by a random amount -stroke color graphic primitive stroke color -strokewidth value graphic primitive stroke width -swirl degrees swirl image pixels about the center -texture filename name of texture to tile onto the image background -threshold value threshold the image -tile filename tile image when filling a graphic primitive -transform affine transform image -transparent color make this color transparent within the image -treedepth value color tree depth -trim trim image edges -type type image type -undercolor color annotation bounding box color -units type PixelsPerInch, PixelsPerCentimeter, or Undefined -unsharp geometry sharpen the image -verbose print detailed information about the image -version print version information -view FlashPix viewing transforms -virtual-pixel method Constant, Edge, Mirror, or Tile -wave geometry alter an image along a sine wave -white-point point chomaticity white point -write filename write images to this file By default, the image format of `file' is determined by its magic number. To specify a particular image format, precede the filename with an image format name and a colon (i.e. ps:image) or specify the image type as the filename suffix (i.e. image.ps). Specify 'file' as '-' for standard input or output.

Have not found a merging option but there must be one somewhere (need to a color filter too). --Sven 10:07, 15 Sep 2006 (NZST)

The flatten has been tested and works, just need to add colour filters now --Sven 10:10, 15 Sep 2006 (NZST)

Not really sure what you're wanting to do here, but you should be able to just extract any channels you want and compose them into a new image any way you like. Imagenagick is very powerful and you can do any kind of image manipulation with it --Nad 09:16, 15 Sep 2006 (NZST)

I have a 16-bit microarray two channel image that is of proprietary format. I want to be able to convert it to a PNG without relying on proprietary software (which I dont have). I think imagemagick will be able to do it, but a subjective call by me will be needed to increase brightness and add red/green filters to the white spots.

It's much more flexiable using ImageMagick from PERL (PerlMagick) because then you can handle multiple channels etc as separate images and maniulate them with imageMagick methods at runtime, then write to any format at the end. --Nad 16:25, 15 Sep 2006 (NZST)

Yes that would be a nice way --Sven 17:30, 15 Sep 2006 (NZST)

File:Red.png

plus

File:Green.png

=

File:Merged.png

--Sven 17:11, 15 Sep 2006 (NZST)

Upper, lower case issues

This code snippet works for lower and upper case extensions converting to lower --Sven 15:16, 3 February 2011 (PST)

# Use a BASH shell loop
in=jpg
out=jpg
dir=LowRes
DEBUG=''

## Check directory exists
if [ ! -d $dir ] ; then
  mkdir $dir
fi

## Loop on all case insensitive file extensions 
for file in `ls | grep -i jpg$`
do
  ## Store upper version of $in as a variable
  inUpper=$(echo $in | tr [[:lower:]] [[:upper:]])
  
  ## Sanity check;
  if [ $DEBUG ]; then
    echo $inUpper
  fi

  echo "[ Converting $file ]"
  if [ $(echo $file | grep $inUpper) ] ; then
    if [ $DEBUG ]; then
      echo U: $file 
    fi
    convert "$file" -resize 800x600 -quality 0 $dir/"${file%%\.$inUpper}.$out"
  else
    if [ $DEBUG ]; then
      echo L: $file
    fi
    convert "$file" -resize 800x600 -quality 0 $dir/"${file%%\.$in}.$out"
  fi
done