[ome-devel] ScanR importer

[Rubén Muñoz]

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;
>>>        }