Stack operations overhaul?

[lechristophe]

Hi,

I'd like to propose some small changes and upgrades to the way ImageJ/Fiji
manipulates stacks. I'm quite aware that most ImageJ developers are focused
on higher-level stuff and that the most likely answer will be "it's open
source, code it yourself", but I'm unfortunately still unable to do it for
now. I nonetheless think these would make day-to-day use of ImageJ more
easy, so I ask.

The behavior of various stack tools (Image>Stacks>Tools in Fiji, don't know
which ones are preset in vanilla ImageJ) is a bit inconsistent at the
moment, regarding slice labels. I'm talking about these (maintained by
Jean-Yves): http://fiji.sc/Stack_Manipulation.  "Concatenate" keeps the
labels form the input stacks, but "Interleave" does not. Would it be
possible to update the various tools so that they always keep the labels
when possible?

Also, it would be nice if Colors>Split Channels was able to keep the slice
labels too, maybe adding a suffix like -Ch00, -Ch01 etc. in the respective
output stacks, rather than just removing all labels.

Lastly, the way Stacks>Images to Stack deals with images of different sizes
is great (detecting them and offering to unify canvas size with various
options). Would it be possible to have the same options in
File>Import>Image Sequence, in order to be able to import a whole folder
with varying image sizes the same way?

Thanks for all the work,

Christophe

--
Christophe Leterrier
Researcher
Axonal Domains Architecture Team
CRN2M CNRS UMR 7286
Aix Marseille University, France

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[dscho]

Hi Christophe,

On Tue, 1 Apr 2014, Christophe Leterrier wrote:

> I'd like to propose some small changes and upgrades to the way ImageJ/Fiji
> manipulates stacks. I'm quite aware that most ImageJ developers are focused
> on higher-level stuff and that the most likely answer will be "it's open
> source, code it yourself", but I'm unfortunately still unable to do it for
> now.

This is actually one of the most excellent opportunities you have to get
your feet wet: you have the motivation, the capability, and the help you
need.

> The behavior of various stack tools (Image>Stacks>Tools in Fiji, don't know
> which ones are preset in vanilla ImageJ) is a bit inconsistent at the
> moment, regarding slice labels. I'm talking about these (maintained by
> Jean-Yves): http://fiji.sc/Stack_Manipulation.  "Concatenate" keeps the
> labels form the input stacks, but "Interleave" does not. Would it be
> possible to update the various tools so that they always keep the labels
> when possible?

The different stack tools are really different plugins, grouped into a single
.jar because they share purpose. "Concatenate" is actually no longer among
them because Wayne implemented the functionality in ImageJ 1.x itself, so
we removed it.

But the Sorter is still there, and it keeps the labels. Here is how it is
done:

https://github.com/fiji/fiji/blob/6f95b6117b6ad68658806b00d2612e1311f0ba97/src-plugins/Stack_Manipulation/src/main/java/Stack_Sorter.java#L219

To fix the "Interleave" plugin, you will therefore have to find all
invocations of the `addSlice()` method in the respective source code:

https://github.com/fiji/fiji/blob/6f95b6117b6ad68658806b00d2612e1311f0ba97/src-plugins/Stack_Manipulation/src/main/java/Stack_Interleaver.java#L54

and change the `null` appropriately. For example, in line 54, it should
call

        stack3.addSlice(stack1.getSliceLabel(i), ip3);

instead of

        stack3.addSlice(null, ip3);

To get started with this project, I would suggest following this
screencast:
https://www.youtube.com/watch?v=XyfE_fVphCs&list=UUOXCsWKZNGez9QOQMWw-Qww
(but work on https://github.com/fiji/fiji instead of
https://github.com/fiji/ImageJA).

I am happy to help you with all obstacles you encounter in that project.

Ciao,
Johannes

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[Jean-Yves Tinevez]

> Hi,
>
> I'd like to propose some small changes and upgrades to the way ImageJ/Fiji
> manipulates stacks. I'm quite aware that most ImageJ developers are focused
> on higher-level stuff and that the most likely answer will be "it's open
> source, code it yourself", but I'm unfortunately still unable to do it for
> now. I nonetheless think these would make day-to-day use of ImageJ more
> easy, so I ask.
>
> The behavior of various stack tools (Image>Stacks>Tools in Fiji, don't
> know which ones are preset in vanilla ImageJ) is a bit inconsistent at the
> moment, regarding slice labels. I'm talking about these (maintained by
> Jean-Yves): http://fiji.sc/Stack_Manipulation.  "Concatenate" keeps the
> labels form the input stacks, but "Interleave" does not. Would it be
> possible to update the various tools so that they always keep the labels
> when possible?
>
> Also, it would be nice if Colors>Split Channels was able to keep the slice
> labels too, maybe adding a suffix like -Ch00, -Ch01 etc. in the respective
> output stacks, rather than just removing all labels.
>
> Lastly, the way Stacks>Images to Stack deals with images of different
> sizes is great (detecting them and offering to unify canvas size with
> various options). Would it be possible to have the same options in
> File>Import>Image Sequence, in order to be able to import a whole folder
> with varying image sizes the same way?
>

Hi all

I'll look into it. Christophe is right, these are heavily used tools in
most users everyday scientific life. Are the original authors around?
The challenge will be to mavenize them all first.
Please be patient.
cheers
jy

--
Jean-Yves Tinevez
PFID - Imagopole
Institut Pasteur
25-28, rue du Docteur Roux
75724 Paris cedex 15
France
mob: [phone]
tel: [phone]
fax: [phone]


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