[ome-devel] ScanrReader deactivated wells

[Melissa Linkert]

Hi Rubén,

> One again need some help with ScanrReader. 
> 
> You know that the Olympus ScanR software is not longer maintained, but quite popular here. 
> And a user found a configuration that prevents your importer to work properly. Not an error but wrong images in the wrong Series. 
> 
> What happened is, some wells were software-deactivated and images were missing, but the experiment_descriptor.xml still indicates all labels.
> 
> I am uploading and example 12-05-25_009.zip to your dev.loci.wisc.edu. 
> 
> Example is the label (A1) exists in the descriptor file and the importer counts with the file to exists, but ends up using the next available image for that well. 
> 
> I tried to fix this myself in a previous version by increasing the variable 'next' when a file is not found (in the main loop).
> This created several null positions in the array 'tiffs' that can be written black (with an zeroed buffer in the TiffWriter).

As always, thank you for the report.

I've written a fix for this, as you can see here:

https://github.com/melissalinkert/bioformats/commit/27ee0cf9856d3a833d32f1d9215963ab980bbb73

...but do note that the trunk build does not yet include this fix.  At
latest, the upcoming 4.4 release of Bio-Formats should include this fix.

Regards,
-Melissa

On Thu, May 31, 2012 at 04:36:20PM +0200, Rubén Muñoz wrote:
> Hi Melissa, 
> 
> One again need some help with ScanrReader. 
> 
> You know that the Olympus ScanR software is not longer maintained, but quite popular here. 
> And a user found a configuration that prevents your importer to work properly. Not an error but wrong images in the wrong Series. 
> 
> What happened is, some wells were software-deactivated and images were missing, but the experiment_descriptor.xml still indicates all labels.
> 
> I am uploading and example 12-05-25_009.zip to your dev.loci.wisc.edu. 
> 
> Example is the label (A1) exists in the descriptor file and the importer counts with the file to exists, but ends up using the next available image for that well. 
> 
> I tried to fix this myself in a previous version by increasing the variable 'next' when a file is not found (in the main loop).
> This created several null positions in the array 'tiffs' that can be written black (with an zeroed buffer in the TiffWriter).
> 
> However I believe that there's a better way to do this. 
> 
> Thanks again for your help, 
> 
> Rubén
> 
> 
> 
>