[ome-devel] ADF images of BD Pathway Bioimager

[Shawn Garbett]

On Apr 29, 2010, at 1:40 PM, Jason H wrote:

>> The raw microscopy information is stored in a proprietary file, which is the
>> adf file. BD Pathway has not shared a specification for the adf file, and it
>> is subject to change at the whim of the BD. The Experiment.exp file that is
>> exported from this is a text file in a known format.
> 
> Hi Shawn,
> 
> Thanks a lot for the info.
> 
>> Support for the adf file could be added, but it would just use it to locate
>> the experiment.exp file in the same directory.
> 
> Then why are there as many .adf files as the number of dyes used in a
> scanning run
> in each well directory?  For a 96-well experiment with 3 dyes, we have
> 288 .adf files
> of varying byte sizes.  If one single experiment.exp file serves the
> purpose, why
> bother with so many useless files scattering around?  Just thinking out loud.
> 
> My real purpose to see what's inside of a .adf file is to look for a
> "stencil" file for each
> dye.  The attached stencil.png is an example of what I mean by a
> stencil file and
> cells.png is the original image from which stencil.png is derived.


So are you using the BD to segment the images, then wanting to pull the data into ImageJ? Right now the bio-formats importer is not pulling in any of the image processing that BD is doing locally, just the captured raw data. 

This met our needs, as we're doing our processing externally and then we're going to store the results in OMERO as a stack. It's my understanding that the BD image processing is in a proprietary binary format.There's a long shot of a chance that it might be a known format, even then this would require some work to support.

Shawn Garbett <shawn.p.garbett at vanderbilt.edu>
Vanderbilt Cancer Biology
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