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

[Scherer, Kathrin]

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<mailto: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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