[ome-users] Assorted metadata/tile parsing fixes #859

[Melissa Linkert]

Hi Lewis,

> Thanks for your response, I saw the proposed changes to the FV1000Reader.  Based on your response, I should have asked the question differently.  Is the timestamp information in the .oib file accessible with a few modifications to FV1000Reader, or will there need to be changes to other scripts which are associated with these *Reader files?  I suppose I am asking these questions to get an idea of how time consuming the solution to the problem will be.  I am also simply interested in learning something new.  
>

Yes, this is localized to the FV1000Reader class.  I would not expect
there to be changes to other classes in order to address the issue, nor
would this impact the way in which Bio-Formats is called by other software.

Regards,
-Melissa

On Fri, Feb 28, 2014 at 03:31:42PM +0000, Kraft, Lewis James wrote:
> Hi,
> 
> Thanks for your response, I saw the proposed changes to the FV1000Reader.  Based on your response, I should have asked the question differently.  Is the timestamp information in the .oib file accessible with a few modifications to FV1000Reader, or will there need to be changes to other scripts which are associated with these *Reader files?  I suppose I am asking these questions to get an idea of how time consuming the solution to the problem will be.  I am also simply interested in learning something new.  
> 
> I have no formal education in programming, and have learned everything I know about it by reading information online. In the course of my graduate career I ran into the need to learn how to do computer programming in order to analyze large microscopy datasets like FRET, FRAP, single particle tracking, and high content imaging screens.  I taught myself how to program in MATLAB, and would consider my knowledge of that language very functional, but perhaps not elegant.  One of the fruits of my labor has been the development of an open source utility for the analysis of FRAP datasets called FRAP-Toolbox.  I am using the Bio-Formats Java library to import the microscopy images and metadata.  See www.fraptoolbox.com for additional details on that (I would also appreciate any feedback you may have).  I am currently in the process of trying to get this tool published in the PLoS Comp Biol journal.  
> 
> Programming has been a very rewarding experience, it is interesting, and it is intellectually challenging. I am continually trying to learn new things that I can use in the future.  For example, I have been trying to learn something about the way Bio-Formats works and the Java language more generally.
> 
> Best,
> Lewis
> 
> -----Original Message-----
> From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Roger Leigh
> Sent: Friday, February 28, 2014 3:23 AM
> To: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Assorted metadata/tile parsing fixes #859
> 
> On 27/02/14 15:22, Kraft, Lewis James wrote:
> > Hi Melissa,
> >
> > Thanks for taking a look at this.  The FV1000 dataset that I uploaded originally should have a varying time increment (I believe after the 20th plane).  Out of curiosity, do you think the problem is in the FV1000Reader.java file?  Let me know if you need me to re-send the test dataset.
> 
> If you look at the changes in the PR, you'll see that there are indeed changes to the FV1000Reader to make it support PlaneDeltaT:
> 
> https://github.com/openmicroscopy/bioformats/pull/859/files
> 
> 
> Regards,
> Roger
> 
> --
> Dr Roger Leigh -- Open Microscopy Environment Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
> 
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