[ome-users] Andor tif data to OME-tif conversion

[Andrew Patterson]

Hi Juergen,

I think the problem might be 'convert'. I have the vague memory that it only works for certain bit depths of TIFF file.

Try using 'tiffcomment' from the Bio-Formats tools.

Usage:
tiffcomment [-set comment] [-edit] file1 [file2 ...]

If using the '-set' option, the new TIFF comment must be specified.
The commment may take any of the following forms:

  * the text of the comment, e.g. 'new comment!'
  * the name of the file containing the text of the comment, e.g. 'file.xml'
  * '-', to enter the comment using stdin.  Entering a blank line will
    terminate reading from stdin.

So:
> convert -comment "@header_info.txt" test.tif test_new.tif
would become something like:
> cp test.tif test_new.tif
> tiffcomment -set 'header_info.txt' test_new.tif


Hope this helps,

Andrew


On 8 Mar 2012, at 14:51, Juergen Helmers wrote:

> Hi,
> 
> I have image data from a screen using an Andor IQ2 instrument. The image data seems to be 16-bit and can be imported into Omero resulting in images with the correct number of channels (here two, red and green). 
> 
> BUT:
> 
> The image are part of a screen of a 96 well plate. per well there are 9 ROI, each stack of multi-channel image files. What I would like to do is import the images as a screen, resulting in a plate of images incorporating the x,y information to place the images inside the grid of the 96 well plate. In addition I have setup a rails application converting CSV annoation sfile to a postgres database and I would like to add the annoation to the metadata before input. 
> 
> this was the plan:
> 
> convert Andor tif file to OME-tif file adding the screen > plate > acquisition > well > ROI information to the header
> 
> When I try to rewrite the Exif information of any Andor file it results in a broken file:
> 
> exiv2 -pa test.tif > header_info.txt
> convert -comment "@header_info.txt" test.tif test_new.tif
> 
> When I import the new tif file although the extracted and rewritten header information are identical the file when imported into Omero is a black and white single channel image. I have used this method and used software before to rewrite molecular devices files to create OME-tif files.
> 
> Has anyone ever dealt with Andor images in order to make them part of a screen, or has some tips on which software to use to rewrite the tif header of Andor files?
> 
> Cheers
> Juergen
> 
> 
> -- 
> Dr. Juergen Helmers
> Chief Developer | webnow | http://www.web-now.de
> email:juergen.helmers at gmail.com | tel:+49 30 37301306 | skype: helmerj 
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20120308/88a6a9ba/attachment.html>