Troubles in opening .lif Leica images

[BROUILLY NICOLAS]

Dear all,

I'm currently experimenting some troubles in opening .lif Leica Images.

I'm running last version of ImageJ, ImageJ64 anf FIJI with last version of LOCI. I'm using a Mac OS X Lion 10.7.5 (11G56), 3,1 GHz Intel Core i5, 16 Go 1333 MHz DDR3, AMD Radeon HD 6970M 1024 MB).

I also tried on 3 different computers (all Mac).

The problem is when I try to open the file whatever the option (hyperstack, standard ImageJ, Metadata only, Data browser or Image 5D) the software bugs and I can read "Expected positive value for ExcitationWavelength; got null" in the ImageJ/FIJI status bar and I have the following "Exception" window that pops up :

java.lang.ClassCastException: ome.xml.model.Polygon cannot be cast to ome.xml.model.Rectangle
at loci.formats.ome.OMEXMLMetadataImpl.setRectangleID(OMEXMLMetadataImpl.java:14051)
at loci.formats.meta.FilterMetadata.setRectangleID(FilterMetadata.java:3122)
at loci.formats.in.LIFReader$ROI.storeROI(LIFReader.java:1892)
at loci.formats.in.LIFReader.initMetadata(LIFReader.java:871)
at loci.formats.in.LIFReader.initFile(LIFReader.java:431)
at loci.formats.FormatReader.setId(FormatReader.java:1238)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:184)
at ij.IJ.runPlugIn(IJ.java:151)
at ij.IJ.runPlugIn(IJ.java:140)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:243)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
at ij.IJ.runUserPlugIn(IJ.java:184)
at ij.IJ.runPlugIn(IJ.java:151)
at ij.IJ.runPlugIn(IJ.java:140)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:430)
at ij.io.Opener.openImage(Opener.java:304)
at ij.io.Opener.openImage(Opener.java:325)
at ij.io.Opener.open(Opener.java:140)
at ij.io.Opener.openAndAddToRecent(Opener.java:240)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
at java.lang.Thread.run(Thread.java:680)

When I re-installed ImageJ with MBF from the begining the problem is still here but now the "Exception" window shows this :

java.lang.NullPointerException
at loci.formats.in.LeicaHandler.startElement(LeicaHandler.java:759)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:501)
at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:179)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1343)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2756)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:647)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:198)
at loci.common.XMLTools.parseXML(XMLTools.java:277)
at loci.common.XMLTools.parseXML(XMLTools.java:252)
at loci.formats.in.LIFReader.initMetadata(LIFReader.java:332)
at loci.formats.in.LIFReader.initFile(LIFReader.java:315)
at loci.formats.FormatReader.setId(FormatReader.java:901)
at loci.plugins.importer.Importer.run(Importer.java:267)
at loci.plugins.LociImporter.run(LociImporter.java:77)
at ij.IJ.runUserPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:152)
at ij.IJ.runPlugIn(IJ.java:141)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:249)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
at ij.IJ.runUserPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:152)
at ij.IJ.runPlugIn(IJ.java:141)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:413)
at ij.io.Opener.openImage(Opener.java:288)
at ij.io.Opener.openImage(Opener.java:309)
at ij.io.Opener.open(Opener.java:138)
at ij.io.Opener.openAndAddToRecent(Opener.java:224)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
at java.lang.Thread.run(Thread.java:680)

I hope I've been clear enough to you to help me out with this issue.

Nicolas Brouilly, PhD Student
Equipe Gieseler, "Pathologies du muscle chez C. elegans"

Centre de Génétique et de Physiologie Moléculaires et Cellulaires
UMR CNRS 5534
Université Claude Bernard Lyon 1
Bâtiment Gregor Mendel, 5ème étage
16, rue Raphaël Dubois
F-69622 Villeurbanne Cedex

[hidden email]<mailto:[hidden email]>
Lab : +0033 (0)4 72 43 29 48
Cel : +0033 (0)6 42 91 53 19




--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Nicolas,

> I'm currently experimenting some troubles in opening .lif Leica
> Images.

You have discovered a bug in Bio-Formats. Would you be willing to send us a
sample non-working dataset? You can use Fiji's Help > Upload Sample Image
command to send one, as long as it is less than 250MB. It will be very
helpful for us to debug the problem.

Thanks,
Curtis


On Wed, Dec 19, 2012 at 11:04 AM, BROUILLY NICOLAS <
[hidden email]> wrote:

> Dear all,
>
> I'm currently experimenting some troubles in opening .lif Leica Images.
>
> I'm running last version of ImageJ, ImageJ64 anf FIJI with last version of
> LOCI. I'm using a Mac OS X Lion 10.7.5 (11G56), 3,1 GHz Intel Core i5, 16
> Go 1333 MHz DDR3, AMD Radeon HD 6970M 1024 MB).
>
> I also tried on 3 different computers (all Mac).
>
> The problem is when I try to open the file whatever the option
> (hyperstack, standard ImageJ, Metadata only, Data browser or Image 5D) the
> software bugs and I can read "Expected positive value for
> ExcitationWavelength; got null" in the ImageJ/FIJI status bar and I have
> the following "Exception" window that pops up :
>
> java.lang.ClassCastException: ome.xml.model.Polygon cannot be cast to
> ome.xml.model.Rectangle
> at
> loci.formats.ome.OMEXMLMetadataImpl.setRectangleID(OMEXMLMetadataImpl.java:14051)
> at
> loci.formats.meta.FilterMetadata.setRectangleID(FilterMetadata.java:3122)
> at loci.formats.in.LIFReader$ROI.storeROI(LIFReader.java:1892)
> at loci.formats.in.LIFReader.initMetadata(LIFReader.java:871)
> at loci.formats.in.LIFReader.initFile(LIFReader.java:431)
> at loci.formats.FormatReader.setId(FormatReader.java:1238)
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
> at loci.plugins.in.Importer.showDialogs(Importer.java:141)
> at loci.plugins.in.Importer.run(Importer.java:79)
> at loci.plugins.LociImporter.run(LociImporter.java:81)
> at ij.IJ.runUserPlugIn(IJ.java:184)
> at ij.IJ.runPlugIn(IJ.java:151)
> at ij.IJ.runPlugIn(IJ.java:140)
> at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:243)
> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
> at ij.IJ.runUserPlugIn(IJ.java:184)
> at ij.IJ.runPlugIn(IJ.java:151)
> at ij.IJ.runPlugIn(IJ.java:140)
> at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:430)
> at ij.io.Opener.openImage(Opener.java:304)
> at ij.io.Opener.openImage(Opener.java:325)
> at ij.io.Opener.open(Opener.java:140)
> at ij.io.Opener.openAndAddToRecent(Opener.java:240)
> at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
> at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
> at java.lang.Thread.run(Thread.java:680)
>
> When I re-installed ImageJ with MBF from the begining the problem is still
> here but now the "Exception" window shows this :
>
> java.lang.NullPointerException
> at loci.formats.in.LeicaHandler.startElement(LeicaHandler.java:759)
> at
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:501)
> at
> com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:179)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1343)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2756)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:647)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
> at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
> at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
> at
> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
> at
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
> at
> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
> at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
> at javax.xml.parsers.SAXParser.parse(SAXParser.java:198)
> at loci.common.XMLTools.parseXML(XMLTools.java:277)
> at loci.common.XMLTools.parseXML(XMLTools.java:252)
> at loci.formats.in.LIFReader.initMetadata(LIFReader.java:332)
> at loci.formats.in.LIFReader.initFile(LIFReader.java:315)
> at loci.formats.FormatReader.setId(FormatReader.java:901)
> at loci.plugins.importer.Importer.run(Importer.java:267)
> at loci.plugins.LociImporter.run(LociImporter.java:77)
> at ij.IJ.runUserPlugIn(IJ.java:185)
> at ij.IJ.runPlugIn(IJ.java:152)
> at ij.IJ.runPlugIn(IJ.java:141)
> at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:249)
> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
> at ij.IJ.runUserPlugIn(IJ.java:185)
> at ij.IJ.runPlugIn(IJ.java:152)
> at ij.IJ.runPlugIn(IJ.java:141)
> at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:413)
> at ij.io.Opener.openImage(Opener.java:288)
> at ij.io.Opener.openImage(Opener.java:309)
> at ij.io.Opener.open(Opener.java:138)
> at ij.io.Opener.openAndAddToRecent(Opener.java:224)
> at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
> at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
> at java.lang.Thread.run(Thread.java:680)
>
> I hope I've been clear enough to you to help me out with this issue.
>
> Nicolas Brouilly, PhD Student
> Equipe Gieseler, "Pathologies du muscle chez C. elegans"
>
> Centre de Génétique et de Physiologie Moléculaires et Cellulaires
> UMR CNRS 5534
> Université Claude Bernard Lyon 1
> Bâtiment Gregor Mendel, 5ème étage
> 16, rue Raphaël Dubois
> F-69622 Villeurbanne Cedex
>
> [hidden email]<mailto:[hidden email]>
> Lab : +0033 (0)4 72 43 29 48
> Cel : +0033 (0)6 42 91 53 19
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[grigetta]

"I'm currently experimenting some troubles in opening .lif Leica Images.
I'm running last version of ImageJ, ImageJ64 anf FIJI with last version of LOCI. I'm using a Mac OS X"
I am having the same problem. I was wondering if the bug had been fixed in the mean time. I'll be happy to upload my files if it helps.
Anna

[JimmiB]

I encountered issues when opening them in windows.  
Solved by replacing loci_tools.jar with the newest version. Sounds like you have done this already.  Try a PC if you have one on hand.

However,

I am running into similar issues trying to run macros to without getting a list of errors similar to what you have posted.
Not sure if this is related to the .lif format.  
Leica seems to make things more difficult than they need be.

Does anyone know how to extract time stamps from these files?

[ctrueden]

Hi JimmyB,

> Does anyone know how to extract time stamps from these files?

Does this macro accomplish what you are looking for?
https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/loci-plugins/utils/macros/planeTimings.txt

Regards,
Curtis


On Tue, Feb 26, 2013 at 7:05 PM, JimmiB <[hidden email]> wrote:

> I encountered issues when opening them in windows.
> Solved by replacing loci_tools.jar with the newest version. Sounds like you
> have done this already.  Try a PC if you have one on hand.
>
> However,
>
> I am running into similar issues trying to run macros to without getting a
> list of errors similar to what you have posted.
> Not sure if this is related to the .lif format.
> Leica seems to make things more difficult than they need be.
>
> Does anyone know how to extract time stamps from these files?
>
>
>
> --
> View this message in context:
> http://imagej.1557.n6.nabble.com/Troubles-in-opening-lif-Leica-images-tp5001217p5001892.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[JimmiB]

Hi Curtis,

Thanks for the reply.

Curtis Rueden wrote

Does this macro accomplish what you are looking for?
https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/loci-plugins/utils/macros/planeTimings.txt

I found that in my search for some kind of solution and can't get it to work.
I think one of the problem with .lif files is they are often comprised of multiple-independent image stacks.

In the ideal world things would be simplified by having a consistent time between frames, however the LAS software seems to find this a challenge.

Cheers,
James

[ctrueden]

Hi James,

> I found that in my search for some kind of solution and can't get it
> to work. I think one of the problem with .lif files is they are often
> comprised of multiple-independent image stacks.

Try using the following macro functions to extract the delta information
from all stacks, rather than only the first:

Ext.getSeriesCount(numberOfStacks) -- obtains the number of image stacks
Ext.setSeries(imageStackOfInterest) -- sets the active image stack to the
given index

In this way, you can loop over all the "series" (i.e., image stacks) to
obtain all time deltas.

For a full list of functions, run Plugins > LOCI > Bio-Formats Macro
Extensions.

If you still have trouble, please let us know.

> In the ideal world things would be simplified by having a consistent
> time between frames, however the LAS software seems to find this a
> challenge.

We actually have logic in Bio-Formats to average the time deltas, so that
it can still populate ImageJ's "Frame Interval" with a reasonable value.

Personally I think it is useful that some file formats such as LIF and
OME-XML make it possible to explicitly record your time deltas. There are
certainly cases where it is scientifically valuable to do so, especially as
we get more and more into the realm of continuous acquisition & analysis
iterations (i.e., acquire each next frame differently based on on-the-fly
analysis of previous frame).

Regards,
Curtis


On Wed, Feb 27, 2013 at 12:27 AM, JimmiB <[hidden email]> wrote:

> Hi Curtis,
>
> Thanks for the reply.
>
>
> Curtis Rueden wrote
> > Does this macro accomplish what you are looking for?
> >
> https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/loci-plugins/utils/macros/planeTimings.txt
>
> I found that in my search for some kind of solution and can't get it to
> work.
> I think one of the problem with .lif files is they are often comprised of
> multiple-independent image stacks.
>
> In the ideal world things would be simplified by having a consistent time
> between frames, however the LAS software seems to find this a challenge.
>
> Cheers,
> James
>
>
>
> --
> View this message in context:
> http://imagej.1557.n6.nabble.com/Troubles-in-opening-lif-Leica-images-tp5001217p5001895.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[hxssbi]

We are having the same problems.  We are looking forward to a fix.

Hyla

[ctrueden]

Hi Hyla,

> We are having the same problems.  We are looking forward to a fix.

I assume you are talking about problems with newer Leica LIF files?

If the issue still persists, can you please report it on the ome-users
mailing list?
    http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/

Thanks,
Curtis


On Thu, Feb 28, 2013 at 5:33 PM, hxssbi <[hidden email]> wrote:

> We are having the same problems.  We are looking forward to a fix.
>
> Hyla
>
>
>
> --
> View this message in context:
> http://imagej.1557.n6.nabble.com/Troubles-in-opening-lif-Leica-images-tp5001217p5001924.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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