[ome-devel] ScanR importer

[Melissa Linkert]

Hi Rubén,

Thank you for uploading another dataset.  r6890
(http://dev.loci.wisc.edu/trac/java/changeset/6890) seems to handle that
dataset properly, and does not cause problems with the other datasets
that I have.  If you could please verify that those changes work for
you, I would appreciate it.

Even with r6890, you will still see several extra wells with all black images.  I have filed a ticket for this problem and CC'd you, but note that it will be a little over a week before I will be able to investigate the problem further.  In case anyone else is interested, the ticket can be viewed here:

http://dev.loci.wisc.edu/trac/java/ticket/550

Regards,
-Melissa

On Mon, Sep 06, 2010 at 10:15:06AM +0200, Rubén Muñoz wrote:
> Hi Melissa, 
> 
> On Sep 2, 2010, at 6:18 PM, Melissa Linkert wrote:
> 
> > Hi Rubén,
> > 
> >> I have tested the current LSM Importer and it is doing fine with multi-position scans.
> > 
> > I'm glad to hear it.
> > 
> >> I have introduced some changes that work for us, but might be not adecuated. You will see that:
> >> 	- The wellRows has to be set, otherwise the uniqueRows may not be a good count in these cases. 
> >> 	- "timeloop count" is used to prevent the execution of nTimepoints = list.length / (nChannels * nWells * nPos * nSlices); 
> >> 	- next variable is always increased even when an image is not found
> > 
> > In principle, these changes look fine.  They are, however, causing a few
> > of the datasets that I have to throw exceptions during initialization.
> 
> My modifications in ScanrReader.java are not good enough, I do not exactly know to proceed.
> I should give you information about the ScanR cDNA labels, they are only set for those wells selected for acquisition.
> 
> Labels "A1     B1 B2" are a valid label set for a 8,96 & 384 well plates. 
> Sorry I do not know how to guess the layout of the plate (total columns and rows) in these cases. But I am after it.
> 
> Please let me know if you have any question.
> 
> Rubén
> 
> > 
> >> With all this I get lots of black images during conversion to multiple file OME-TIF. That's not perfect but they can be deleted afterwards.
> > 
> > I will have to think on how best to do it, but I think we can
> > change the ScanR reader to prevent this problem.
> > 
> >> Please permit me to upload one of these to the FTP with name "scanRskippedWells.zip", and let me know if I can help with something else.
> > 
> > Of course you may upload as much data as you like.  Once you have
> > uploaded the data, just let me know - I can then work on updating your
> > changes so that they work with all of the datasets that we have so far.
> 
> I recently uploaded scanRskippedWells.zip to your SFTP
> 
> > 
> > Regards,
> > -Melissa
> > 
> > On Thu, Sep 02, 2010 at 11:36:50AM +0200, Rubén Muñoz wrote:
> >> Hi Melissa,
> >> 
> >> I have tested the current LSM Importer and it is doing fine with multi-position scans.
> >> That will be incredibly useful here to create OME.TIFs, in combination with bfconvert.
> >> 
> >> I found some possible improvement for the ScanR importer.
> >> We have always provided with sets that have all the wells, but one of our users skipped some wells with the microscope.
> >> 
> >> That was not converting because of two things:
> >> 	- The loops iterated only until the number of real acquired wells nWells.
> >> 	- The tiff array was filled sequentially.
> >> 
> >> Therefore the imageName is calculated always sequentially.
> >> 
> >> I have introduced some changes that work for us, but might be not adecuated. You will see that:
> >> 	- The wellRows has to be set, otherwise the uniqueRows may not be a good count in these cases. 
> >> 	- "timeloop count" is used to prevent the execution of nTimepoints = list.length / (nChannels * nWells * nPos * nSlices); 
> >> 	- next variable is always increased even when an image is not found
> >> 
> >> With all this I get lots of black images during conversion to multiple file OME-TIF. That's not perfect but they can be deleted afterwards.
> >> 
> >> Please permit me to upload one of these to the FTP with name "scanRskippedWells.zip", and let me know if I can help with something else.
> >> 
> >> Best regards
> >> 
> >> Rubén
> >> 
> >> 
> >> diff bioformats/components/bio-formats/src/loci/formats/in/ScanrReader.java bioformats.ruben/components/bio-formats/src/loci/formats/in/ScanrReader.java 
> >> 300,301c300,306
> >> <     if (wellRows * wellColumns == 0) {
> >> <       if (wellCount <= 96) {
> >> ---
> >>>    //if (wellRows * wellColumns == 0) {
> >>>    // FIXME: Three only formats are enforced
> >>>      if (wellCount <= 8) {
> >>>        wellColumns = 2;
> >>>        wellRows = 4;
> >>>      }
> >>>      else if (wellCount <= 96) {
> >> 302a308
> >>>        wellRows = 8;
> >> 305a312
> >>>        wellRows = 8;
> >> 307,309c314,316
> >> <       wellRows = wellCount / wellColumns;
> >> <       if (wellRows * wellColumns < wellCount) wellRows++;
> >> <     }
> >> ---
> >>>      //wellRows = wellCount / wellColumns;
> >>>      //if (wellRows * wellColumns < wellCount) wellRows++;
> >>>    //}
> >> 318a326
> >>> 
> >> 365a374
> >>> 	else next++;
> >> 522a532,534
> >>>        else if (key.equals("timeloop count")) {
> >>>          core[0].sizeT = Integer.parseInt(value) + 1;
> >>>        }
>