How do I disable the automatic generation of Hyperstacks?

[arnim.jenett]

Hi,
in the newer versions of ImageJ my stacks (lsm) open up as Hyperstacks. This is pretty disturbing, because
- I'd rather work on the original channels - as before,
- I can not see both channels at the same time anymore,
- the color scheme (red-green) is not suited for presentation because it is not readable for colorblind (check out this page: http://jfly.iam.u-tokyo.ac.jp/color/)
- a whole bunch of macros I wrote for image analysis is not working anymore.

Could this please changed back?
Or can we get a toggle somewhere to switch off this function?

I think most of us ImageJ-users love ImageJ for the direct access to their data, now with the hyperstacks there was an an unwanted layer introduced into  the data access. I think this was a step in the wrong direction. Am I alone with this perception?
Best,
aRnim

[jmutterer]

aRnim,

You can get multiple windows by reverting to an older version of lsm
toolbox, like 4.0b, and opening your lsm files with the toolbox instead of
using the file/open command.
However, I think opening multichannel images as hyperstacks makes sense.
Stack.* macro functions set makes working with hyperstacks pretty easy, and
definitely easier than working with multiple image windows.

Jerome


On Thu, Jun 19, 2008 at 8:20 PM, aRnim <[hidden email]> wrote:

> Hi,
> in the newer versions of ImageJ my stacks (lsm) open up as Hyperstacks.
> This
> is pretty disturbing, because
> - I'd rather work on the original channels - as before,
> - I can not see both channels at the same time anymore,
> - the color scheme (red-green) is not suited for presentation because it is
> not readable for colorblind (check out this page:
> http://jfly.iam.u-tokyo.ac.jp/color/)
> - a whole bunch of macros I wrote for image analysis is not working
> anymore.
>
> Could this please changed back?
> Or can we get a toggle somewhere to switch off this function?
>
> I think most of us ImageJ-users love ImageJ for the direct access to their
> data, now with the hyperstacks there was an an unwanted layer introduced
> into  the data access. I think this was a step in the wrong direction. Am I
> alone with this perception?
> Best,
> aRnim
>
> --
> View this message in context:
> http://www.nabble.com/How-do-I-disable-the-automatic-generation-of-Hyperstacks--tp18015027p18015027.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[Wayne Rasband]

> Hi,
> in the newer versions of ImageJ my stacks (lsm) open up as
> Hyperstacks. This
> is pretty disturbing, because
> - I'd rather work on the original channels - as before,
> - I can not see both channels at the same time anymore,
> - the color scheme (red-green) is not suited for presentation because
> it is
> not readable for colorblind (check out this page:
> http://jfly.iam.u-tokyo.ac.jp/color/)
> - a whole bunch of macros I wrote for image analysis is not working
> anymore.
>
> Could this please changed back?
> Or can we get a toggle somewhere to switch off this function?
>
> I think most of us ImageJ-users love ImageJ for the direct access to
> their
> data, now with the hyperstacks there was an an unwanted layer
> introduced
> into  the data access. I think this was a step in the wrong direction.
> Am I
> alone with this perception?

You can use the Image>Color>RGB Split command to split off the original
channels.

-wayne

[dscho]

Hi,

On Thu, 19 Jun 2008, Jerome Mutterer wrote:

> However, I think opening multichannel images as hyperstacks makes sense.
> Stack.* macro functions set makes working with hyperstacks pretty easy,
> and definitely easier than working with multiple image windows.

I think the point aRnim was making is that it broke his scripts.  I could
imagine that he is not the only one having this problem, but that he may
be the only one sending a mail to this list saying so.

Ciao,
Dscho

[Mark Longair-2]

aRnim <[hidden email]> wrote:
[..]
> I think most of us ImageJ-users love ImageJ for the direct
> access to their data, now with the hyperstacks there was an an
> unwanted layer introduced into the data access. I think this
> was a step in the wrong direction. Am I alone with this
> perception?
[..]

I like the interface for viewing multiple channels in a
hyperstack now that I'm used to it, but I think the introduction
of this new type of image has caused a great deal of confusion
to the users that I know, and potentially creates a lot of work
for people who write plugins.  I hope it will be helpful if I
describe some of the problems that I've seen people have, since
there seems to have been very little discussion of this on the
list so far.

 - Confusion over the terminology - the terms "hyperstack" seems
   to be clearly defined in the documentation as an image (a
   single ImagePlus object?) with 4 or 5 dimensions.  "composite
   image" isn't clear to me, though, since it seems to be
   sometimes used synomymously with "hyperstack" and many people
   seem to use the term (presumably incorrectly?) to mean a
   COLOR_RGB image.

 - If a user loads a file for a multi-channel image and for the
   first time gets a hyperstack rather than multiple images, the
   first thing they're likely to want to do is to turn it back
   into the form the they are used to, as Arnim described.  It's
   not obvious how to do this, however, since the "Hyperstack to
   Stack" command suprisingly produces a single stack with
   slices of the original two channels interleaved.  ("RGB
   Split" has the right effect here, as the documentation
   explains and Wayne mentioned, but since what people see
   doesn't look like an RGB image to them, it's likely to take
   some trial and error to discover this.)

 - Paths through the user interface that used to work for people
   no longer do.  For example, many people are accustomed to
   using "RGB Merge" to produce an RGB image from multiple image
   stacks, each representing a channel.  If they do this now
   then there is a new option ("Create Composite Image") which
   is selected by default.  This option causes the error:

     java.lang.IllegalArgumentException: Argument out of range: 1
     at ij.ImageStack.getProcessor(ImageStack.java:232)
     at ij.plugin.RGBStackMerge.createComposite(RGBStackMerge.java:142)
     at ij.plugin.RGBStackMerge.mergeStacks(RGBStackMerge.java:102)
     ...

   Furthermore, one of the source images will have been affected
   so that subsequently running "RGB Merge" without that option
   selected will fail until the source images are reloaded.

   If the user's source image is a hyperstack rather than
   multiple images (and they persist even though they can't
   select different images for different channels) then the same
   error occurs.  If they don't have the "Create Composite
   Image" option selected then the results are a composite image
   of double the depth with interleaved slices from both
   channels - again, suprising behaviour.

 - The "Channels" dialog is essential for working with
   hyperstacks, but takes people some time to discover.  Perhaps
   either this could be launched from a button alongside the new
   channel slider or be given a more suggestive name in the
   menus?  e.g. if were renamed "Channel Display Options" and
   moved to the top of the hyperstacks menu?  (Also the "More"
   popup menu is essentially redundant since, if I understand
   correctly, only one of "Make Composite" and "Convert to RGB"
   will do anything for any given image, and "Open HeLa Cells"
   doesn't need to be there.)

 - It's not clear what plugin writers have to do in order to
   update their code to properly support hyperstacks.
   (Obviously there are a huge number of plugins that will need
   to be updated in this way.)  It would make life slightly
   easier if there were were a method in ij.CompositeImage that
   returned an array of one ImagePlus object per channel to
   create a simple way to apply your old code to CompositeImage
   objects without running into the "interleaved slices"
   problem.  I've attached a patch against ImageJ 1.41e that
   adds this method, and a new source tree with the patch
   applied can be found here:

      http://longair.net/ij141e-src-with-split-channels.zip

The "RGB Merge" issue is clearly just a bug, but I think it's
worth mentioning in the same context since it affects the user
experience of hyperstacks.

regards,
mark

P.S. For people having problems with this kind of thing, the
documentation here is helpful on the subject hyperstacks:

   http://rsb.info.nih.gov/ij/docs/menus/image.html#hyperstacks

[ctrueden]

Hi aRnim,

If you use the Bio-Formats Importer plugin (
http://www.loci.wisc.edu/ome/formats.html), you can choose whether to
display the result as a hyperstack, a standard (2D) ImageJ window, an
Image5D window (if you have the Image5D plugin installed), a View5D window
(if you have the View5D plugin installed), or a Data Browser window (a 5D
visualization plugin bundled with the Bio-Formats plugins).

-Curtis

On Thu, Jun 19, 2008 at 7:20 PM, aRnim <[hidden email]> wrote:

> Hi,
> in the newer versions of ImageJ my stacks (lsm) open up as Hyperstacks.
> This
> is pretty disturbing, because
> - I'd rather work on the original channels - as before,
> - I can not see both channels at the same time anymore,
> - the color scheme (red-green) is not suited for presentation because it is
> not readable for colorblind (check out this page:
> http://jfly.iam.u-tokyo.ac.jp/color/)
> - a whole bunch of macros I wrote for image analysis is not working
> anymore.
>
> Could this please changed back?
> Or can we get a toggle somewhere to switch off this function?
>
> I think most of us ImageJ-users love ImageJ for the direct access to their
> data, now with the hyperstacks there was an an unwanted layer introduced
> into  the data access. I think this was a step in the wrong direction. Am I
> alone with this perception?
> Best,
> aRnim
>
> --
> View this message in context:
> http://www.nabble.com/How-do-I-disable-the-automatic-generation-of-Hyperstacks--tp18015027p18015027.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[Wayne Rasband]

> Hi,
> in the newer versions of ImageJ my stacks (lsm) open up as
> Hyperstacks. This
> is pretty disturbing, because
> - I'd rather work on the original channels - as before,
> - I can not see both channels at the same time anymore,
> - the color scheme (red-green) is not suited for presentation because
> it is
> not readable for colorblind (check out this page:
> http://jfly.iam.u-tokyo.ac.jp/color/)
> - a whole bunch of macros I wrote for image analysis is not working
> anymore.
>
> Could this please changed back?
> Or can we get a toggle somewhere to switch off this function?

You can change back to the previous behavior by replacing the
LSM_Reader.jar file in the plugins folder with the previous version
(v1.40), which is available at

    http://rsb.info.nih.gov/ij/plugins/download/misc/LSM_Reader.jar

-wayne

[Mark Longair-2]

Arnim,

aRnim <[hidden email]> wrote:
[..]
> - I can not see both channels at the same time anymore,

I wasn't sure if you meant by this:

  (a) having channels in separate windows or
  (b) seeing the channels merged

As mentioned earlier, (a) is "RGB Split", which I guess you'll
want to assign a shortcut to.  You can do (b) by bringing up the
"Channels" dialog with Shift-z and changing the selection from
"Color" to "Composite".

> - the color scheme (red-green) is not suited for presentation because it is
> not readable for colorblind (check out this page:
> http://jfly.iam.u-tokyo.ac.jp/color/)
[..]

The red and green lookup tables are taken from your LSM file, I
think, or has that behaviour changed for you recently?  You can
change the red channel to magenta with Image > Lookup Tables >
Magenta or typing lmagent[down-arrow][enter]

Personally, I think these particular aspects are rather simpler
with the hyperstack, but the other things do bother me.

regards,
mark

[arnim.jenett]

>> - I can not see both channels at the same time anymore,
>
> I wasn't sure if you meant by this:
>
>   (a) having channels in separate windows or
>   (b) seeing the channels merged
Actually I meant both. And what you describe here I implemented into my macros. Btw, it's not that easy as it looks, because the behavior of "RGB Split" changed as well: It prepends a "C[1-9]-" to the original file name... Well, nothing is as constant as change. to cope with this:
(basename=file name - suffix)
if (matches(substring(basename, 0, 3), "C[1-9]-")) {
        basename=substring(basename,3, lengthOf(basename));
}
...
(stack=file name)
if (Stack.isHyperstack) {
        run("RGB Split");
        RED="C2-"+stack;
        GREEN="C1-"+stack;
        ...
}
        ...
        run("RGB Merge...", "red=["+RED+"] green=["+GREEN+"] blue="RED");

>
> As mentioned earlier, (a) is "RGB Split", which I guess you'll
> want to assign a shortcut to.  You can do (b) by bringing up the
> "Channels" dialog with Shift-z and changing the selection from
> "Color" to "Composite".
The macro command for this is 'run("Stack to RGB")'. Stack to RGB??? Well, the RGB is still a stack, but ... never mind.
I think this command's name is not picked very well.
>
>> - the color scheme (red-green) is not suited for presentation because it is
>> not readable for colorblind (check out this page:
>> http://jfly.iam.u-tokyo.ac.jp/color/)
> [..]
>
> The red and green lookup tables are taken from your LSM file, I
> think, or has that behaviour changed for you recently?  You can
> change the red channel to magenta with Image > Lookup Tables >
> Magenta or typing lmagent[down-arrow][enter]
The macros command is run ("Magenta");

Best,
aRnim