[OpenSPIM] OMETiffHandler fix

Tue Apr 21 15:05:08 CDT 2015

Hello,
Ulrik, thank you for updating the OMETiffHandler.  I have to admit, I don't
know what to do with the file you have linked, though.  I haven't used
Maven before.  Is that the only way to incorporate this change into Fiji?
Thank you,
Aurelia

On Mon, Apr 20, 2015 at 6:00 PM, <openspim-request at openspim.org> wrote:

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> Today's Topics:
>
>    1. Re: open SPIM acquisition error (Ulrik G?nther)
>    2. Re: open SPIM acquisition error (Johannes Schindelin)
>    3. 64-bit Fiji Memory Limit Issue (Roberts, Thomas)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: 20 Apr 2015 10:23:42 +0200
> From: Ulrik G?nther <guenther at mpi-cbg.de>
> To: Johannes Schindelin <johannes.schindelin at gmx.de>
> Cc: Aurelia Honerkamp-Smith <aureliaomega at gmail.com>,
>         openspim at openspim.org
> Subject: Re: [OpenSPIM] open SPIM acquisition error
> Message-ID: <2D47F005-0963-4704-B2CC-ACD0D4044D0B at mpi-cbg.de>
> Content-Type: text/plain; charset="utf-8"
>
>   Hello Aurelia and Johannes,
>
>
> I modified the OMETiffHandler to use the new Units API of BioFormats, you
> can find the changes at?
> https://github.com/skalarproduktraum/SPIMAcquisition/tree/OMEUnitFixes
>
>
> Question to Johannes: Do you want a pull request for that? The issue I?m
> currently having is that it works just fine in Fiji with the MM update
> site, but not with the latest MM nightly, as it brings an older ome-xml
> version. Suggestions?
>
>
> cheers,
>
>
> ulrik
>
>
>
>
> ?
> Ulrik G?nther, Dipl.-Phys.
> PhD Student
> MOSAIC Group & Tomancak Lab,?Center of Systems Biology Dresden
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstr. 108, D-01307 Dresden, Germany
>
>
>
> E-Mail:?guenther at mpi-cbg.de
>
>
>
>
> > On Apr 17, 2015, at 10:10 PM, Johannes Schindelin <
> johannes.schindelin at gmx.de> wrote:
> >
> >
> > Hi Aurelia,
> >
> >
> > On 2015-04-17 16:56, Aurelia Honerkamp-Smith wrote:
> >
> >
> >> java.lang.NoSuchMethodError:
> >>
> loci.formats.meta.IMetadata.setPixelsPhysicalSizeX(Lome/xml/model/primitives/PositiveFloat;I)V
> >>
> >>
> >>
> >
> >
> > It would appear as if OMERO might have broken Bio-Formats'?
> > backwards-compatibility once again... Exceptions like this one mean that?
> > the method setPixelsPhysicalSizeX(PositiveFloat) was available at?
> > compile time but is no longer available at runtime.
> >
> >
> > And indeed, it looks as if IMetadata by virtue of extending?
> > ome.xml.meta.MetadataStore defines only the following?
> > setPixelsPhysicalSizeX() method:
> >
> >
> > public abstract void setPixelsPhysicalSizeX(ome.units.quantity.Length,?
> > int);
> >
> >
> > I fear that we will have to update the SPIMAcquisition plugin in a hurry?
> > to conform with the new Bio-Formats version that was so overzealously?
> > uploaded to the Fiji update site despite breaking backwards?
> > compatibility in a rather blatant way.
> >
> >
> > My calendar is densely packed, though, so I have no idea when I will get?
> > around to fix it (hint: help appreciated).
> >
> >
> > Ciao,
> > Johannes
> >
> >
> > _______________________________________________
> > OpenSPIM mailing list
> > OpenSPIM at openspim.org
> > http://openspim.org/mailman/listinfo/openspim
> >
> >
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> ------------------------------
>
> Message: 2
> Date: Mon, 20 Apr 2015 11:26:49 +0200
> From: Johannes Schindelin <johannes.schindelin at gmx.de>
> To: Ulrik G?nther <guenther at mpi-cbg.de>
> Cc: Aurelia Honerkamp-Smith <aureliaomega at gmail.com>,
>         openspim at openspim.org
> Subject: Re: [OpenSPIM] open SPIM acquisition error
> Message-ID: <cf359e135dae45adea047be9c310649b at www.dscho.org>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Hi Ulrik,
>
> On 2015-04-20 10:23, Ulrik G?nther wrote:
>
> > Question to Johannes: Do you want a pull request for that?
>
> Whenever some code in OpenSPIM has been improved, or for that matter, in
> any Open Source software I maintain, I want a Pull Request. Otherwise
> the software would not improve but deteriorate, wouldn't it?
>
> So was that a trick question?
>
> > The issue I?m currently having is that it works just fine in Fiji with
> > the MM
> > update site, but not with the latest MM nightly, as it brings an older
> > ome-xml version. Suggestions?
>
> My suggestion is not new.
>
> My suggestion is to finally work together on having *the same* software
> versions in all OpenSPIM setups, by using the update site. We already
> have a beautiful update site, but nobody took care so far to get it back
> up-to-date, right? So now everybody and her dog has to work just as hard
> as everybody else to get to a working state, and nobody benefits from
> anybody else's work (the Pull Requests that have been opened and merged
> have been a really nice exception).
>
> I know that it is typically highly discouraged in scientific work to
> work with other groups: after all, you could write papers, and even
> scoop other groups, instead of working on something that benefits them
> as well as yourself, right? This, however, is not the idea behind
> OpenSPIM. The idea of OpenSPIM is that when everybody works a little,
> everybody benefits a *lot*.
>
> So let's work everybody a little on the software. Preferably in a way
> that other people do not have to solve the same problem that you solved,
> *again*. Rather, in a way where each problem is solved such that nobody
> else has to bother with the same problem. Whether you share your
> solution as a mail to this list, as an edit to the wiki, as a Pull
> Request, just share it.
>
> Then we all will benefit.
>
> Ciao,
> Johannes
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 20 Apr 2015 15:31:57 +0000
> From: "Roberts, Thomas" <thomas.roberts.10 at ucl.ac.uk>
> To: "openspim at openspim.org" <openspim at openspim.org>
> Subject: [OpenSPIM] 64-bit Fiji Memory Limit Issue
> Message-ID: <1429543916741.90268 at ucl.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi everyone,
>
>
> This is probably a wider issue with Fiji than OpenSPIM, but I was
> wondering if anyone else encountered the same problem we are having.
>
>
> For reference, we are running 64-bit Windows 7 on a monster machine with
> 64GB RAM, an Intel Xeon E5-2650 and an nVidia Quadro 5000.
>
>
> We generally run the 32-bit version of OpenSPIM for acquisition, but
> opening large image datasets (such as the ones in the Registation tutorial:
> http://openspim.org/Registration) results in Fiji reaching its memory
> limit. Because of this, I downloaded the 64-bit version of OpenSPIM/MM/Fiji
> in an attempt to increase the memory limit.
>
>
> If I set the memory limit to a large value (20,000 MB) by going to Edit >
> Options > Memory & Threads, I get the same error message, as below:
>
>
> Loading C:\Users\SPIM\Documents\OpenSPIM Dresden
> Data\tiffs\\spim_TL05_Angle0.tif
> >>>>>>>>>>>>>>>>>>>>>>>>>>>
> <Out of memory>
> <All available memory (505MB) has been>
> <used. To make more available, use the>
> <Edit>Options>Memory & Threads command.>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>
>
> This is really odd, because if I go to Help > About ImageJ, it says that
> 13MB out of 20000MB (<1%) is in use. Put another way, Fiji accepts that I
> want to increase the memory limit, but it still doesn't use more than 505MB
> of memory.
>
> As a sanity check, I have installed 64-bit Fiji on my office computer and
> I can open the Registration tutorial data there, but my personal computer
> is really slow at manipulating the large datasets!
>
> Has anyone else experienced this problem? Or does anyone have any
> suggestions for how to solve the issue?
>
> It's really frustrating as our behemoth PC refuses to do what it was
> bought to do!
>
> Many thanks in advance for any replies.
> Tom Roberts
>
> -----
> Research Associate
> UCL Centre for Advanced Biomedical Imaging
> thomas.roberts.10 at ucl.ac.uk
>
>
>
>
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