[ome-users] Opening 3D PALM images using Bio-Formats

[Douglas Richardson]

Sorry Katherine,

I should have qualified that by saying we've only used the work around for
2D PALM experiments.  Sorry it doesn't work on 3D as well.

-Doug

On Wed, Apr 22, 2015 at 11:26 AM, Scherer, Kathrin <k.scherer at ucl.ac.uk>
wrote:

>  Dear Doug,
>
>
>
> Thank you for your email. I converted my files to .lsm5 in ZEN and opend
> the files in Icy/ImageJ using the Bio-Formats and now the colour channel is
> being recognized. Unfortunately the software does still not recognize that
> the data set is supposed to be 3D and only seems to open the first slice.
>
>
>
> Kind regards,
>
>
>
> Kathrin
>
>
>
> *From:* ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] *On
> Behalf Of *Douglas Richardson
> *Sent:* 21 April 2015 18:50
> *To:* Melissa Linkert; OME User Support List
> *Subject:* Re: [ome-users] Opening 3D PALM images using Bio-Formats
>
>
>
> If you save/convert the PALM file to an .lsm5 in ZEN, you should be able
> to open it with Bioformats.
>
> -Doug
>
>
>
> On Tue, Apr 21, 2015 at 10:17 AM, Melissa Linkert <
> melissa at glencoesoftware.com> wrote:
>
> Hi Kathrin,
>
> > Last week I tried to open 3D PALM/STORM images that I recorded in ZEN
> Black with a Zeiss ELYRA microscope in Icy, but the images are not being
> loaded in the correct way. I end up with a black image in the viewer,
> whilst I am expecting a Z-stack through a cell.
> >
> > I have already contacted the Icy support team about this, but they told
> me that it is a problem with the Bio-Formats plugin. I assume this
> relatively new image format might just not be supported yet?
> >
> > I saved the files in the .czi format. Normally .czi files seem to open
> okay in Icy. I have also tried to open SIM files in the past and it was no
> problem.
> > It would be great if you could let me know if there is a way to open
> this file type in Icy or Fiji.
> >
> > I will also upload a couple of example files onto your QA system.
>
> Thank you very much for reporting this problem, and for uploading sample
> files.  We are aware of issues with opening PALM data from the Elyra
> systems, and there is an open ticket for this on our issue tracking
> system:
>
> http://trac.openmicroscopy.org/ome/ticket/12469
>
> There unfortunately isn't a workaround at the moment, but we will update
> the ticket as we make progress on fixing this.  If you would like to be
> automatically notified of updates, please let us know and we'll CC you.
>
> Regards,
> -Melissa
>
>
> On Tue, Apr 21, 2015 at 12:05:08PM +0000, Scherer, Kathrin wrote:
> > Hi,
> >
> > Last week I tried to open 3D PALM/STORM images that I recorded in ZEN
> Black with a Zeiss ELYRA microscope in Icy, but the images are not being
> loaded in the correct way. I end up with a black image in the viewer,
> whilst I am expecting a Z-stack through a cell.
> >
> > I have already contacted the Icy support team about this, but they told
> me that it is a problem with the Bio-Formats plugin. I assume this
> relatively new image format might just not be supported yet?
> >
> > I saved the files in the .czi format. Normally .czi files seem to open
> okay in Icy. I have also tried to open SIM files in the past and it was no
> problem.
> > It would be great if you could let me know if there is a way to open
> this file type in Icy or Fiji.
> >
> > I will also upload a couple of example files onto your QA system.
> >
> > Many thanks,
> >
> > Kathrin
> >
> > Kathrin Scherer PhD BSc
> > Light Microscopy Officer
> >
> > Room 2.10
> > MRC Laboratory for Molecular Cell Biology (LMCB)
> > University College London
> > Gower Street
> > London, WC1E 6BT
> >
> >
> >
> >
>
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> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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