Analyze 7.5 in Fiji and ImageJ

[James Ewing]

Hi All -  

I wrote a little C program to generate image files in Analyze 7.5 format.  It's the final filter of some processing pipes that I use on MRI data.  Vanilla 64-bit ImageJ reads and displays the multi-image Analyze 7.5 files just fine as a stack of images.  Fiji doesn't recognize the files as having multiple images, but just displays the first image of the pack of images.  I'd like to use Fiji throughout, but I keep running into this problem of not being able to read my Analyze files.  Now, if Ii read my file in using ImageJ and write it out to a tiff file, Fiji reads the multi-image file as having multiple images, but even if I read the file in using ImageJ and write it out as an Analyze 7.5 file using ImageJ, Fiji doesn't see that it is a multi-image file.  Any ideas?

- Jim
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[dscho]

Hi James,

On Fri, 15 Mar 2013, James Ewing wrote:

> I wrote a little C program to generate image files in Analyze 7.5
> format.  It's the final filter of some processing pipes that I use on
> MRI data.  Vanilla 64-bit ImageJ reads and displays the multi-image
> Analyze 7.5 files just fine as a stack of images.  Fiji doesn't
> recognize the files as having multiple images, but just displays the
> first image of the pack of images.  I'd like to use Fiji throughout, but
> I keep running into this problem of not being able to read my Analyze
> files.  Now, if Ii read my file in using ImageJ and write it out to a
> tiff file, Fiji reads the multi-image file as having multiple images,
> but even if I read the file in using ImageJ and write it out as an
> Analyze 7.5 file using ImageJ, Fiji doesn't see that it is a multi-image
> file.  Any ideas?

I can only guess that the Analyze_Reader_Writer is outdated in Fiji...
Ideally, the author would either notify me or anybody else working on Fiji
when there is a new version...

In the meantime, I updated it from the ImageJ update site [*1*] and
uploaded a new .jar to the Fiji update site.

Does this fix your problem?

Ciao,
Johannes

Footnote *1*: http://imagej.net/plugins/analyze.html

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[James Ewing]

Hi Johannes - Thanks for your effort, but that didn't do the trick.  I think there's a difference in how the two programs look at the header information. To take my code out of the picture, I read a tiff multi-image file in to ImageJ (vanilla) and saved it as an Analyze 7.5 file from vanilla ImageJ.  Fiji didn't see that file as an Analyze 7.5 multi-image file.  I then read that multi-image tiff file into Fiji, which it saw as a multi-image file, and saved it from Fiji as an Analyze 7.5 file.  Fiji _did_ see that file as a multi-image file.  I'll diff the headers to see what's different between the two and get back to you, but you should know that there is definitely a difference in how the two programs see the Analyze 7.5 format.

 - Jim
 
On Mar 16, 2013, at 12:44 PM, Johannes Schindelin wrote:

> Hi James,
>
> On Fri, 15 Mar 2013, James Ewing wrote:
>
>> I wrote a little C program to generate image files in Analyze 7.5
>> format.  It's the final filter of some processing pipes that I use on
>> MRI data.  Vanilla 64-bit ImageJ reads and displays the multi-image
>> Analyze 7.5 files just fine as a stack of images.  Fiji doesn't
>> recognize the files as having multiple images, but just displays the
>> first image of the pack of images.  I'd like to use Fiji throughout, but
>> I keep running into this problem of not being able to read my Analyze
>> files.  Now, if Ii read my file in using ImageJ and write it out to a
>> tiff file, Fiji reads the multi-image file as having multiple images,
>> but even if I read the file in using ImageJ and write it out as an
>> Analyze 7.5 file using ImageJ, Fiji doesn't see that it is a multi-image
>> file.  Any ideas?
>
> I can only guess that the Analyze_Reader_Writer is outdated in Fiji...
> Ideally, the author would either notify me or anybody else working on Fiji
> when there is a new version...
>
> In the meantime, I updated it from the ImageJ update site [*1*] and
> uploaded a new .jar to the Fiji update site.
>
> Does this fix your problem?
>
> Ciao,
> Johannes
>
> Footnote *1*: http://imagej.net/plugins/analyze.html

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[dscho]

Hi,

On Sat, 16 Mar 2013, James Ewing wrote:

> On Mar 16, 2013, at 12:44 PM, Johannes Schindelin wrote:
>
> > On Fri, 15 Mar 2013, James Ewing wrote:
> >
> >> I wrote a little C program to generate image files in Analyze 7.5
> >> format.  It's the final filter of some processing pipes that I use on
> >> MRI data.  Vanilla 64-bit ImageJ reads and displays the multi-image
> >> Analyze 7.5 files just fine as a stack of images.  Fiji doesn't
> >> recognize the files as having multiple images, but just displays the
> >> first image of the pack of images.  I'd like to use Fiji throughout,
> >> but I keep running into this problem of not being able to read my
> >> Analyze files.  Now, if Ii read my file in using ImageJ and write it
> >> out to a tiff file, Fiji reads the multi-image file as having
> >> multiple images, but even if I read the file in using ImageJ and
> >> write it out as an Analyze 7.5 file using ImageJ, Fiji doesn't see
> >> that it is a multi-image file.  Any ideas?
> >
> > I can only guess that the Analyze_Reader_Writer is outdated in Fiji...
> > Ideally, the author would either notify me or anybody else working on
> > Fiji when there is a new version...
> >
> > In the meantime, I updated it from the ImageJ update site [*1*] and
> > uploaded a new .jar to the Fiji update site.
>
> Thanks for your effort, but that didn't do the trick.

Hmm. A couple of questions: Do you have any plugin installed in the
vanilla ImageJ that might want to read the file?

If not, does uninstalling Analyze_Reader_Writer-2.0.0-SNAPSHOT.jar in Fiji
(after Help>Update Fiji, click "Advanced Mode" and type "Analyze" in the
search box, then mark it and click "Uninstall", then "Apply changes") help
it?

Ciao,
Johannes

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[James Ewing]

Johannes -

The uninstall did the trick.  I'm wondering why.  Was there a legacy file that wasn't getting overwritten?

Thanks.  BTW - the header files differed in a few spots.  I didn't track down what fields they were.  Can do if needed.

- Jim

On Mar 16, 2013, at 2:09 PM, Johannes Schindelin wrote:

> Hi,
>
> On Sat, 16 Mar 2013, James Ewing wrote:
>
>> On Mar 16, 2013, at 12:44 PM, Johannes Schindelin wrote:
>>
>>> On Fri, 15 Mar 2013, James Ewing wrote:
>>>
>>>> I wrote a little C program to generate image files in Analyze 7.5
>>>> format.  It's the final filter of some processing pipes that I use on
>>>> MRI data.  Vanilla 64-bit ImageJ reads and displays the multi-image
>>>> Analyze 7.5 files just fine as a stack of images.  Fiji doesn't
>>>> recognize the files as having multiple images, but just displays the
>>>> first image of the pack of images.  I'd like to use Fiji throughout,
>>>> but I keep running into this problem of not being able to read my
>>>> Analyze files.  Now, if Ii read my file in using ImageJ and write it
>>>> out to a tiff file, Fiji reads the multi-image file as having
>>>> multiple images, but even if I read the file in using ImageJ and
>>>> write it out as an Analyze 7.5 file using ImageJ, Fiji doesn't see
>>>> that it is a multi-image file.  Any ideas?
>>>
>>> I can only guess that the Analyze_Reader_Writer is outdated in Fiji...
>>> Ideally, the author would either notify me or anybody else working on
>>> Fiji when there is a new version...
>>>
>>> In the meantime, I updated it from the ImageJ update site [*1*] and
>>> uploaded a new .jar to the Fiji update site.
>>
>> Thanks for your effort, but that didn't do the trick.
>
> Hmm. A couple of questions: Do you have any plugin installed in the
> vanilla ImageJ that might want to read the file?
>
> If not, does uninstalling Analyze_Reader_Writer-2.0.0-SNAPSHOT.jar in Fiji
> (after Help>Update Fiji, click "Advanced Mode" and type "Analyze" in the
> search box, then mark it and click "Uninstall", then "Apply changes") help
> it?
>
> Ciao,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[dscho]

Hi James,

On Sat, 16 Mar 2013, James Ewing wrote:

> On Mar 16, 2013, at 2:09 PM, Johannes Schindelin wrote:
>
> > On Sat, 16 Mar 2013, James Ewing wrote:
> >
> >> On Mar 16, 2013, at 12:44 PM, Johannes Schindelin wrote:
> >>
> >>> On Fri, 15 Mar 2013, James Ewing wrote:
> >>>
> >>>> I wrote a little C program to generate image files in Analyze 7.5
> >>>> format.  It's the final filter of some processing pipes that I use on
> >>>> MRI data.  Vanilla 64-bit ImageJ reads and displays the multi-image
> >>>> Analyze 7.5 files just fine as a stack of images.  Fiji doesn't
> >>>> recognize the files as having multiple images, but just displays the
> >>>> first image of the pack of images.
> >>>
> >>> I can only guess that the Analyze_Reader_Writer is outdated in
> >>> Fiji...  Ideally, the author would either notify me or anybody else
> >>> working on Fiji when there is a new version...
> >>>
> >>> In the meantime, I updated it from the ImageJ update site [*1*] and
> >>> uploaded a new .jar to the Fiji update site.
> >>
> >> Thanks for your effort, but that didn't do the trick.
> >
> > Hmm. A couple of questions: Do you have any plugin installed in the
> > vanilla ImageJ that might want to read the file?
> >
> > If not, does uninstalling Analyze_Reader_Writer-2.0.0-SNAPSHOT.jar in
> > Fiji (after Help>Update Fiji, click "Advanced Mode" and type "Analyze"
> > in the search box, then mark it and click "Uninstall", then "Apply
> > changes") help it?
>
> The uninstall did the trick.  I'm wondering why.  Was there a legacy
> file that wasn't getting overwritten?

The problem is that HandleExtraFileTypes detects that you are looking at
an Analyze image and hands of to a special-purpose plugin to read it
because vanilla ImageJ is known to have limitations when it comes to read
.tiff files: there are just way too many extensions to the TIFF (Tagged
Image File Format).

However, in this case, it seems that the limitations are the plugin's and
ImageJ's plain TIFF reader handles your data better than the
special-purpose plugin.

> Thanks.  BTW - the header files differed in a few spots.  I didn't track
> down what fields they were.  Can do if needed.

As you can see here:

https://github.com/fiji/fiji/blob/master/src-plugins/IO_/src/main/java/HandleExtraFileTypes.java#L141

Fiji's HandleExtraFileTypes class looks for the file extension .img or
.hdr and hands off to either Nifti Reader or Analyze Reader.

So if you want to avoid the Analyze Reader, why not simply write to .tiff
files instead?

Ciao,
Johannes

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

[ctrueden]

Hi James,

> I'd like to use Fiji throughout, but I keep running into this problem
> of not being able to read my Analyze files.

The Bio-Formats Importer plugin also supports Analyze 7.5, so you could try
that as another option. (File > Import > Bio-Formats in Fiji.)

Regards,
Curtis


On Sat, Mar 16, 2013 at 2:11 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi James,
>
> On Sat, 16 Mar 2013, James Ewing wrote:
>
> > On Mar 16, 2013, at 2:09 PM, Johannes Schindelin wrote:
> >
> > > On Sat, 16 Mar 2013, James Ewing wrote:
> > >
> > >> On Mar 16, 2013, at 12:44 PM, Johannes Schindelin wrote:
> > >>
> > >>> On Fri, 15 Mar 2013, James Ewing wrote:
> > >>>
> > >>>> I wrote a little C program to generate image files in Analyze 7.5
> > >>>> format.  It's the final filter of some processing pipes that I use
> on
> > >>>> MRI data.  Vanilla 64-bit ImageJ reads and displays the multi-image
> > >>>> Analyze 7.5 files just fine as a stack of images.  Fiji doesn't
> > >>>> recognize the files as having multiple images, but just displays the
> > >>>> first image of the pack of images.
> > >>>
> > >>> I can only guess that the Analyze_Reader_Writer is outdated in
> > >>> Fiji...  Ideally, the author would either notify me or anybody else
> > >>> working on Fiji when there is a new version...
> > >>>
> > >>> In the meantime, I updated it from the ImageJ update site [*1*] and
> > >>> uploaded a new .jar to the Fiji update site.
> > >>
> > >> Thanks for your effort, but that didn't do the trick.
> > >
> > > Hmm. A couple of questions: Do you have any plugin installed in the
> > > vanilla ImageJ that might want to read the file?
> > >
> > > If not, does uninstalling Analyze_Reader_Writer-2.0.0-SNAPSHOT.jar in
> > > Fiji (after Help>Update Fiji, click "Advanced Mode" and type "Analyze"
> > > in the search box, then mark it and click "Uninstall", then "Apply
> > > changes") help it?
> >
> > The uninstall did the trick.  I'm wondering why.  Was there a legacy
> > file that wasn't getting overwritten?
>
> The problem is that HandleExtraFileTypes detects that you are looking at
> an Analyze image and hands of to a special-purpose plugin to read it
> because vanilla ImageJ is known to have limitations when it comes to read
> .tiff files: there are just way too many extensions to the TIFF (Tagged
> Image File Format).
>
> However, in this case, it seems that the limitations are the plugin's and
> ImageJ's plain TIFF reader handles your data better than the
> special-purpose plugin.
>
> > Thanks.  BTW - the header files differed in a few spots.  I didn't track
> > down what fields they were.  Can do if needed.
>
> As you can see here:
>
>
> https://github.com/fiji/fiji/blob/master/src-plugins/IO_/src/main/java/HandleExtraFileTypes.java#L141
>
> Fiji's HandleExtraFileTypes class looks for the file extension .img or
> .hdr and hands off to either Nifti Reader or Analyze Reader.
>
> So if you want to avoid the Analyze Reader, why not simply write to .tiff
> files instead?
>
> Ciao,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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