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opening .flex format images

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Soriano.Joaquim

opening .flex format images

Hi there!

I would like to open stacks of images that are saved in a .flex format.

¿is it possible?, ¿anyone knows how to do it?

Thank you very much in advance.

Joaquim Soriano Felipe.

Confocal Microscopy Unit

Spanish National Cancer Research Centre (CNIO)

Melchor Fernández Almagro,3, E-28029 Madrid, Spain

Phone + 34 917 328 000, exts.: 3161, 3162. [hidden email] <mailto:[hidden email]>

**NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

Melissa Linkert-2

Re: opening .flex format images

Hi Joaquim,

You could use Bio-Formats:

http://loci.wisc.edu/bio-formats/imagej

which supports reading images in many file formats, including Flex.

Regards,
-Melissa

On Wed, Oct 20, 2010 at 10:07:36AM +0200, Soriano.Joaquim wrote:

> Hi there!
>
> I would like to open stacks of images that are saved in a .flex format.
>
> ¿is it possible?, ¿anyone knows how to do it?
>
> Thank you very much in advance.
>
>
>
> Joaquim Soriano Felipe.
>
> Confocal Microscopy Unit
>
> Spanish National Cancer Research Centre (CNIO)
>
> Melchor Fernández Almagro,3, E-28029 Madrid, Spain
>
> Phone + 34 917 328 000, exts.: 3161, 3162. [hidden email] <mailto:[hidden email]>
>
>
>
>
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>
>

Soriano.Joaquim

Re: opening .flex format images

I've just tried LOCI and it didn´t worked (Thank you very much Melissa anyway),
The images I'm trying to open were captured by using a Perkin Elmer, Opera, High content screening system (a high through output confocal microscope). I do not know whether LOCI is unable to open my images or I'm not able to run it properly. When I try to open my flex file the following error occurs: "File is not supported format, a reader plugin is not available, or it was not found.
¿can anyone help me?
I can send a file if anyone is interested/willing to help.
Thank you all!!!

-----Mensaje original-----
De: ImageJ Interest Group [mailto:[hidden email]] En nombre de Melissa Linkert
Enviado el: jueves, 21 de octubre de 2010 0:40
Para: [hidden email]
Asunto: Re: opening .flex format images

Hi Joaquim,

You could use Bio-Formats:

http://loci.wisc.edu/bio-formats/imagej

which supports reading images in many file formats, including Flex.

Regards,
-Melissa

On Wed, Oct 20, 2010 at 10:07:36AM +0200, Soriano.Joaquim wrote:

Melissa Linkert-2

Re: opening .flex format images

Hi Joaquim,

> I do not know whether LOCI is unable to open my images or I'm not able to run it properly. When I try to open my flex file the following error occurs: "File is not supported format, a reader plugin is not available, or it was not found.
> ¿can anyone help me?

It sounds like you opened the file by selecting "File > Open" or by
dragging the file onto the ImageJ toolbar. If you instead select
"Plugin > LOCI > Bio-Formats Importer" and then choose the .flex file, then
the file should be opened correctly.

Regards,
-Melissa

On Thu, Oct 21, 2010 at 10:11:59AM +0200, Soriano.Joaquim wrote:

> I've just tried LOCI and it didn´t worked (Thank you very much Melissa anyway),
> The images I'm trying to open were captured by using a Perkin Elmer, Opera, High content screening system (a high through output confocal microscope). I do not know whether LOCI is unable to open my images or I'm not able to run it properly. When I try to open my flex file the following error occurs: "File is not supported format, a reader plugin is not available, or it was not found.
> ¿can anyone help me?
> I can send a file if anyone is interested/willing to help.
> Thank you all!!!
>
> -----Mensaje original-----
> De: ImageJ Interest Group [mailto:[hidden email]] En nombre de Melissa Linkert
> Enviado el: jueves, 21 de octubre de 2010 0:40
> Para: [hidden email]
> Asunto: Re: opening .flex format images
>
> Hi Joaquim,
>
> You could use Bio-Formats:
>
> http://loci.wisc.edu/bio-formats/imagej
>
> which supports reading images in many file formats, including Flex.
>
> Regards,
> -Melissa
>
> On Wed, Oct 20, 2010 at 10:07:36AM +0200, Soriano.Joaquim wrote:
> > Hi there!
> >
> > I would like to open stacks of images that are saved in a .flex format.
> >
> > ¿is it possible?, ¿anyone knows how to do it?
> >
> > Thank you very much in advance.
> >
> >
> >
> > Joaquim Soriano Felipe.
> >
> > Confocal Microscopy Unit
> >
> > Spanish National Cancer Research Centre (CNIO)
> >
> > Melchor Fernández Almagro,3, E-28029 Madrid, Spain
> >
> > Phone + 34 917 328 000, exts.: 3161, 3162. [hidden email] <mailto:[hidden email]>
> >
> >
> >
> >
> >
> > **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> > **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
> >
> >
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

Soriano.Joaquim

Re: opening .flex format images

Hi Melissa,
I was doing exactly what you reported (dragging the file onto the ImageJ toolbar). Once I used the Bio-Formats Importer, ..., I got a different error!!!
"Sorry, there was a problem during import", and:

" loci.formats.MissingLibraryException: The LuraWave decoding library, lwf_jsdk2.6.jar, is required to decode this file.
Please make sure it is present in your classpath.
at loci.formats.codec.LuraWaveCodec.initialize(LuraWaveCodec.java:153)
at loci.formats.codec.LuraWaveCodec.decompress(LuraWaveCodec.java:85)
at loci.formats.tiff.TiffCompression.decompress(TiffCompression.java:186)
at loci.formats.tiff.TiffParser.getTile(TiffParser.java:584)
at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:709)
at loci.formats.in.FlexReader.openBytes(FlexReader.java:208)
at loci.formats.FormatReader.openBytes(FormatReader.java:739)
at loci.formats.ChannelFiller.getLookupTableComponentCount(ChannelFiller.java:262)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:245)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:279)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
at loci.plugins.in.ImportProcess.setId(ImportProcess.java:652)
at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:513)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
at loci.plugins.in.Importer.showDialogs(Importer.java:125)
at loci.plugins.in.Importer.run(Importer.java:77)
at loci.plugins.LociImporter.run(LociImporter.java:77)
at ij.IJ.runUserPlugIn(IJ.java:183)
at ij.IJ.runPlugIn(IJ.java:150)
at ij.Executer.runCommand(Executer.java:124)
at ij.Executer.run(Executer.java:61)
at java.lang.Thread.run(Thread.java:619)
Caused by: Unable to instantiate service for interface loci.formats.services.LuraWaveService
at loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:152)
at loci.formats.codec.LuraWaveCodec.initialize(LuraWaveCodec.java:150)
... 26 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:150)
... 27 more
Caused by: java.lang.NoClassDefFoundError: com/luratech/lwf/lwfDecoder
at loci.formats.services.LuraWaveServiceImpl.<init>(LuraWaveServiceImpl.java:77)
... 32 more
Caused by: java.lang.ClassNotFoundException: com.luratech.lwf.lwfDecoder
at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
... 33 more

But it seems we are getting close to the solution!!!
Any other idea? Maybe we've just found a bug that has to be fixed (I'll get in touch with the plugin's developer) or something's wrong with my Java.
Thanks for your time!!!

-----Mensaje original-----
De: ImageJ Interest Group [mailto:[hidden email]] En nombre de Melissa Linkert
Enviado el: jueves, 21 de octubre de 2010 15:22
Para: [hidden email]
Asunto: Re: opening .flex format images

Hi Joaquim,

> I do not know whether LOCI is unable to open my images or I'm not able to run it properly. When I try to open my flex file the following error occurs: "File is not supported format, a reader plugin is not available, or it was not found.
> ¿can anyone help me?

It sounds like you opened the file by selecting "File > Open" or by
dragging the file onto the ImageJ toolbar. If you instead select
"Plugin > LOCI > Bio-Formats Importer" and then choose the .flex file, then
the file should be opened correctly.

Regards,
-Melissa

On Thu, Oct 21, 2010 at 10:11:59AM +0200, Soriano.Joaquim wrote:

Ash Dunne

Re: opening .flex format images

Hi,

Have you tried updating your bio-formats trunk build (http://www.loci.wisc.edu/bio-formats/downloads)? I had a problem recently where ImageJ would no longer open DeltaVision files. Turned out downloading the new trunk did the job.

Might be worth a try.

Cheers,

Ash

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Soriano.Joaquim
Sent: 21 October 2010 15:50
To: [hidden email]
Subject: Re: opening .flex format images

Hi Melissa,
I was doing exactly what you reported (dragging the file onto the ImageJ toolbar). Once I used the Bio-Formats Importer, ..., I got a different error!!!
"Sorry, there was a problem during import", and:

" loci.formats.MissingLibraryException: The LuraWave decoding library, lwf_jsdk2.6.jar, is required to decode this file.
Please make sure it is present in your classpath.
at loci.formats.codec.LuraWaveCodec.initialize(LuraWaveCodec.java:153)
at loci.formats.codec.LuraWaveCodec.decompress(LuraWaveCodec.java:85)
at loci.formats.tiff.TiffCompression.decompress(TiffCompression.java:186)
at loci.formats.tiff.TiffParser.getTile(TiffParser.java:584)
at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:709)
at loci.formats.in.FlexReader.openBytes(FlexReader.java:208)
at loci.formats.FormatReader.openBytes(FormatReader.java:739)
at loci.formats.ChannelFiller.getLookupTableComponentCount(ChannelFiller.java:262)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:245)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:279)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
at loci.plugins.in.ImportProcess.setId(ImportProcess.java:652)
at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:513)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
at loci.plugins.in.Importer.showDialogs(Importer.java:125)
at loci.plugins.in.Importer.run(Importer.java:77)
at loci.plugins.LociImporter.run(LociImporter.java:77)
at ij.IJ.runUserPlugIn(IJ.java:183)
at ij.IJ.runPlugIn(IJ.java:150)
at ij.Executer.runCommand(Executer.java:124)
at ij.Executer.run(Executer.java:61)
at java.lang.Thread.run(Thread.java:619)
Caused by: Unable to instantiate service for interface loci.formats.services.LuraWaveService
at loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:152)
at loci.formats.codec.LuraWaveCodec.initialize(LuraWaveCodec.java:150)
... 26 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:150)
... 27 more
Caused by: java.lang.NoClassDefFoundError: com/luratech/lwf/lwfDecoder
at loci.formats.services.LuraWaveServiceImpl.<init>(LuraWaveServiceImpl.java:77)
... 32 more
Caused by: java.lang.ClassNotFoundException: com.luratech.lwf.lwfDecoder
at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
... 33 more

But it seems we are getting close to the solution!!!
Any other idea? Maybe we've just found a bug that has to be fixed (I'll get in touch with the plugin's developer) or something's wrong with my Java.
Thanks for your time!!!

-----Mensaje original-----
De: ImageJ Interest Group [mailto:[hidden email]] En nombre de Melissa Linkert Enviado el: jueves, 21 de octubre de 2010 15:22
Para: [hidden email]
Asunto: Re: opening .flex format images

Hi Joaquim,

> I do not know whether LOCI is unable to open my images or I'm not able to run it properly. When I try to open my flex file the following error occurs: "File is not supported format, a reader plugin is not available, or it was not found.
> ¿can anyone help me?

It sounds like you opened the file by selecting "File > Open" or by dragging the file onto the ImageJ toolbar. If you instead select "Plugin > LOCI > Bio-Formats Importer" and then choose the .flex file, then the file should be opened correctly.

Regards,
-Melissa

On Thu, Oct 21, 2010 at 10:11:59AM +0200, Soriano.Joaquim wrote:

> I've just tried LOCI and it didn´t worked (Thank you very much Melissa
> anyway), The images I'm trying to open were captured by using a Perkin Elmer, Opera, High content screening system (a high through output confocal microscope). I do not know whether LOCI is unable to open my images or I'm not able to run it properly. When I try to open my flex file the following error occurs: "File is not supported format, a reader plugin is not available, or it was not found.
> ¿can anyone help me?
> I can send a file if anyone is interested/willing to help.
> Thank you all!!!
>
> -----Mensaje original-----
> De: ImageJ Interest Group [mailto:[hidden email]] En nombre de
> Melissa Linkert Enviado el: jueves, 21 de octubre de 2010 0:40
> Para: [hidden email]
> Asunto: Re: opening .flex format images
>
> Hi Joaquim,
>
> You could use Bio-Formats:
>
> http://loci.wisc.edu/bio-formats/imagej
>
> which supports reading images in many file formats, including Flex.
>
> Regards,
> -Melissa
>
> On Wed, Oct 20, 2010 at 10:07:36AM +0200, Soriano.Joaquim wrote:
> > Hi there!
> >
> > I would like to open stacks of images that are saved in a .flex format.
> >
> > ¿is it possible?, ¿anyone knows how to do it?
> >
> > Thank you very much in advance.
> >
> >
> >
> > Joaquim Soriano Felipe.
> >
> > Confocal Microscopy Unit
> >
> > Spanish National Cancer Research Centre (CNIO)
> >
> > Melchor Fernández Almagro,3, E-28029 Madrid, Spain
> >
> > Phone + 34 917 328 000, exts.: 3161, 3162. [hidden email]
> > <mailto:[hidden email]>
> >
> >
> >
> >
> >
> > **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> > **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
> >
> >
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
--------------------------------------------------------
This email is confidential and intended solely for the use of the person(s) ('the intended recipient') to whom it was addressed. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Paterson Institute for Cancer Research or the University of Manchester. It may contain information that is privileged & confidential within the meaning of applicable law. Accordingly any dissemination, distribution, copying, or other use of this message, or any of its contents, by any person other than the intended recipient may constitute a breach of civil or criminal law and is strictly prohibited. If you are NOT the intended recipient please contact the sender and dispose of this e-mail as soon as possible.

ctrueden

Re: opening .flex format images

In reply to this post by Soriano.Joaquim

Hi Joaquim,

loci.formats.MissingLibraryException: The LuraWave decoding library,
> lwf_jsdk2.6.jar, is required to decode this file.
> Please make sure it is present in your classpath.
>

Sounds like you have old-style Flex files that use the proprietary LWF
encoding scheme. Unfortunately, the LWF decoder is commercial software,
which we cannot distribute with Bio-Formats.

However, you can get support for reading these files by downloading the
MBF_ImageJ bundle from:
http://www.macbiophotonics.ca/imagej/

The MBF_ImageJ distribution comes with the LWF library, which Bio-Formats
can use to read that type of Flex file. This is possible due to the
generosity of Tony Collins and the McMaster Biophotonics Facility, who
bought a license to redistribute the LWF decoder.

HTH,
Curtis

On Thu, Oct 21, 2010 at 4:50 PM, Soriano.Joaquim <[hidden email]> wrote:

> Hi Melissa,
> I was doing exactly what you reported (dragging the file onto the ImageJ
> toolbar). Once I used the Bio-Formats Importer, ..., I got a different
> error!!!
> "Sorry, there was a problem during import", and:
>
> " loci.formats.MissingLibraryException: The LuraWave decoding library,
> lwf_jsdk2.6.jar, is required to decode this file.
> Please make sure it is present in your classpath.
> at
> loci.formats.codec.LuraWaveCodec.initialize(LuraWaveCodec.java:153)
> at
> loci.formats.codec.LuraWaveCodec.decompress(LuraWaveCodec.java:85)
> at
> loci.formats.tiff.TiffCompression.decompress(TiffCompression.java:186)
> at loci.formats.tiff.TiffParser.getTile(TiffParser.java:584)
> at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:709)
> at loci.formats.in.FlexReader.openBytes(FlexReader.java:208)
> at loci.formats.FormatReader.openBytes(FormatReader.java:739)
> at
> loci.formats.ChannelFiller.getLookupTableComponentCount(ChannelFiller.java:262)
> at loci.formats.ChannelFiller.setId(ChannelFiller.java:245)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
> at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:279)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
> at loci.plugins.in.ImportProcess.setId(ImportProcess.java:652)
> at
> loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:513)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
> at loci.plugins.in.Importer.showDialogs(Importer.java:125)
> at loci.plugins.in.Importer.run(Importer.java:77)
> at loci.plugins.LociImporter.run(LociImporter.java:77)
> at ij.IJ.runUserPlugIn(IJ.java:183)
> at ij.IJ.runPlugIn(IJ.java:150)
> at ij.Executer.runCommand(Executer.java:124)
> at ij.Executer.run(Executer.java:61)
> at java.lang.Thread.run(Thread.java:619)
> Caused by: Unable to instantiate service for interface
> loci.formats.services.LuraWaveService
> at
> loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:152)
> at
> loci.formats.codec.LuraWaveCodec.initialize(LuraWaveCodec.java:150)
> ... 26 more
> Caused by: java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
> at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
> at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
> at
> loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:150)
> ... 27 more
> Caused by: java.lang.NoClassDefFoundError: com/luratech/lwf/lwfDecoder
> at
> loci.formats.services.LuraWaveServiceImpl.<init>(LuraWaveServiceImpl.java:77)
> ... 32 more
> Caused by: java.lang.ClassNotFoundException: com.luratech.lwf.lwfDecoder
> at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
> at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
> ... 33 more
>
> But it seems we are getting close to the solution!!!
> Any other idea? Maybe we've just found a bug that has to be fixed (I'll get
> in touch with the plugin's developer) or something's wrong with my Java.
> Thanks for your time!!!
>
> -----Mensaje original-----
> De: ImageJ Interest Group [mailto:[hidden email]] En nombre de
> Melissa Linkert
> Enviado el: jueves, 21 de octubre de 2010 15:22
> Para: [hidden email]
> Asunto: Re: opening .flex format images
>
> Hi Joaquim,
>
> > I do not know whether LOCI is unable to open my images or I'm not able to
> run it properly. When I try to open my flex file the following error occurs:
> "File is not supported format, a reader plugin is not available, or it was
> not found.
> > ¿can anyone help me?
>
> It sounds like you opened the file by selecting "File > Open" or by
> dragging the file onto the ImageJ toolbar. If you instead select
> "Plugin > LOCI > Bio-Formats Importer" and then choose the .flex file, then
> the file should be opened correctly.
>
> Regards,
> -Melissa
>
> On Thu, Oct 21, 2010 at 10:11:59AM +0200, Soriano.Joaquim wrote:
> > I've just tried LOCI and it didn´t worked (Thank you very much Melissa
> anyway),
> > The images I'm trying to open were captured by using a Perkin Elmer,
> Opera, High content screening system (a high through output confocal
> microscope). I do not know whether LOCI is unable to open my images or I'm
> not able to run it properly. When I try to open my flex file the following
> error occurs: "File is not supported format, a reader plugin is not
> available, or it was not found.
> > ¿can anyone help me?
> > I can send a file if anyone is interested/willing to help.
> > Thank you all!!!
> >
> > -----Mensaje original-----
> > De: ImageJ Interest Group [mailto:[hidden email]] En nombre de
> Melissa Linkert
> > Enviado el: jueves, 21 de octubre de 2010 0:40
> > Para: [hidden email]
> > Asunto: Re: opening .flex format images
> >
> > Hi Joaquim,
> >
> > You could use Bio-Formats:
> >
> > http://loci.wisc.edu/bio-formats/imagej
> >
> > which supports reading images in many file formats, including Flex.
> >
> > Regards,
> > -Melissa
> >
> > On Wed, Oct 20, 2010 at 10:07:36AM +0200, Soriano.Joaquim wrote:
> > > Hi there!
> > >
> > > I would like to open stacks of images that are saved in a .flex format.
> > >
> > > ¿is it possible?, ¿anyone knows how to do it?
> > >
> > > Thank you very much in advance.
> > >
> > >
> > >
> > > Joaquim Soriano Felipe.
> > >
> > > Confocal Microscopy Unit
> > >
> > > Spanish National Cancer Research Centre (CNIO)
> > >
> > > Melchor Fernández Almagro,3, E-28029 Madrid, Spain
> > >
> > > Phone + 34 917 328 000, exts.: 3161, 3162. [hidden email] <mailto:
> [hidden email]>
> > >
> > >
> > >
> > >
> > >
> > > **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los
> ficheros adjuntos, pueden contener informaciÿn protegida para el uso
> exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o
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> and delete all copies.
> > >
> > >
> >
> > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los
> ficheros adjuntos, pueden contener información protegida para el uso
> exclusivo de su destinatario. Se prohíbe la distribución, reproducción o
> cualquier otro tipo de transmisión por parte de otra persona que no sea el
> destinatario. Si usted recibe por error este correo, se ruega comunicarlo al
> remitente y borrar el mensaje recibido.
> > **CONFIDENTIALITY NOTICE** This email communication and any attachments
> may contain confidential and privileged information for the sole use of the
> designated recipient named above. Distribution, reproduction or any other
> use of this transmission by any party other than the intended recipient is
> prohibited. If you are not the intended recipient please contact the sender
> and delete all copies.
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los
> ficheros adjuntos, pueden contener información protegida para el uso
> exclusivo de su destinatario. Se prohíbe la distribución, reproducción o
> cualquier otro tipo de transmisión por parte de otra persona que no sea el
> destinatario. Si usted recibe por error este correo, se ruega comunicarlo al
> remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may
> contain confidential and privileged information for the sole use of the
> designated recipient named above. Distribution, reproduction or any other
> use of this transmission by any party other than the intended recipient is
> prohibited. If you are not the intended recipient please contact the sender
> and delete all copies.
>

Soriano.Joaquim

Re: opening .flex format images

I did as you and Melissa told me and it is definitely working!!!
Thank you very much to all people that answered and to Tony Collins and the McMaster Biophotonics Facility for making it possible.

-----Mensaje original-----
De: ImageJ Interest Group [mailto:[hidden email]] En nombre de Curtis Rueden
Enviado el: jueves, 21 de octubre de 2010 23:32
Para: [hidden email]
Asunto: Re: opening .flex format images

Hi Joaquim,

loci.formats.MissingLibraryException: The LuraWave decoding library,
> lwf_jsdk2.6.jar, is required to decode this file.
> Please make sure it is present in your classpath.
>

Sounds like you have old-style Flex files that use the proprietary LWF
encoding scheme. Unfortunately, the LWF decoder is commercial software,
which we cannot distribute with Bio-Formats.

However, you can get support for reading these files by downloading the
MBF_ImageJ bundle from:
http://www.macbiophotonics.ca/imagej/

The MBF_ImageJ distribution comes with the LWF library, which Bio-Formats
can use to read that type of Flex file. This is possible due to the
generosity of Tony Collins and the McMaster Biophotonics Facility, who
bought a license to redistribute the LWF decoder.

HTH,
Curtis

On Thu, Oct 21, 2010 at 4:50 PM, Soriano.Joaquim <[hidden email]> wrote: