What does ImageJ stand for?

[Alan Hewat-2]

As a grateful user of ImageJ, old enough to have known NIH Image, Sun and
Silicon Graphics software and hardware, I think the name ImageJ is fine as
it is. Obviously many people have contributed, and I have also used Fiji,
which is modestly and amusingly named "Fiji Is Just ImageJ".

The great strengths of the core program are that it is lightweight, runs on
modest hardware and is easy to extend with plugins, so everyone can tailor
it to their own needs while maintaining a coherent base.

Let's not confuse things by changing names to ImageJ1, J2 etc. "Everything
should be as simple as possible".

Alan.
________________________________
Dr Alan Hewat, NeutronOptics,
Grenoble, FRANCE (from phone)
[hidden email]
         +33.476.98.41.68
http://NeutronOptics.com/hewat
_______________________________

>
>>

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

[Curtis Rueden-2]

Hi everyone,

Wayne and I discussed off-list, and agreed that ImageJ2 and the original
ImageJ (a.k.a. ImageJ 1.x) are both official versions of ImageJ. In cases
where the distinction matters, please refer to them respectively as
"ImageJ2" and "ImageJ 1.x" (not ImageJ1). See the P.S. below for further
details.

I have updated the imagej.net website to remove as many usages of the term
ImageJ1 as possible:

https://github.com/imagej/imagej.github.io/commit/a3f228a66418e9e227ed1f472ff747528a4a8135

In the coming days I will work on restoring the ImageJ wiki's project icon
feature, so that each page can have an icon next to its title indicating
its scope, with tooltip giving more information upon mouseover. So e.g.
pages about ImageJ 1.x plugins will have the ImageJ 1.x logo, pages about
ImageJ2 plugins will have the ImageJ2 logo, and pages about plugins bundled
with Fiji will have the Fiji logo. (I may also implement support for pages
belonging to multiple projects -- e.g. a Fiji plugin built on ImageJ2
should probably show both logos.) Any other suggestions for clarifying
these distinctions across the wiki are most welcome.

Wayne Rasband wrote:
> I will try to edit the wiki page.

Looks good. Thank you!

> Thanks for removing the copyright notice. ImageJ is in the public
> domain, so it was inappropriate.

Just to clarify: a copyright notice at the bottom of a webpage declares the
copyright for the website content, not the copyright of any software being
documented. The intent was never to declare any sort of copyright there
relating to the ImageJ programs (neither ImageJ 1.x nor ImageJ2).

> What are the workflow changes that would be needed to eliminate the
> ImageJA repository?

The page https://imagej.net/libs/imageja briefly describes why ImageJA
still exists, and how changes to ImageJ flow from imagej/imagej1 to
imagej/ImageJA to binary builds deployed to OSS Sonatype. The two relevant
CI jobs are:
* https://travis-ci.com/github/imagej/ij1-builds -- generates commits to
ImageJA matching the ImageJ letter releases
* https://travis-ci.org/github/imagej/ImageJA -- builds and deploys ij.jar
in response to changes to ImageJA

A better workflow would be to push changes to the ImageJ repository
whenever you want, and use the SciJava release-version.sh script to cut
letter releases, as described at https://imagej.net/develop/releasing. If
you'd like to discuss it further, I can file an issue on GitHub with more
information, so we don't splinter the discussion thread.

Regards,
Curtis

P.S. Here is a summary of how the ImageJ projects have been named since
2010 when the ImageJ2 project was funded:

* ImageJ2 is a new version of ImageJ, targeting a broader set of scenarios,
and focused on scientific imaging.
* As such, the term "ImageJ" can refer to ImageJ 1.x, ImageJ2, or both
together.
* The term "ImageJ components" refers to any or all software components
(JAR files) in the imagej GitHub organization, with groupId net.imagej --
for example:
    - net.imagej:ij (ImageJ 1.x -- ij.* packages)
    - net.imagej:imagej (ImageJ2 top-level project -- net.imagej.* packages)
    - net.imagej:imagej-common (ImageJ Common -- net.imagej.* packages)
    - net.imagej:imagej-updater (ImageJ Updater -- net.imagej.updater.*
packages)
    - net.imagej:imagej-ops (ImageJ Ops -- net.imagej.ops.* packages)
  E.g. "ImageJ Common is a component of the ImageJ project, and part of
ImageJ2, the redesigned version of ImageJ."
* The program "Fiji" is a distribution of ImageJ (both ImageJ 1.x and
ImageJ2 together).
* The term "Fiji components" refers to software components (JAR files) in
the fiji GitHub organization, with groupId sc.fiji -- e.g.
sc.fiji:TrackMate_.
* We often use the term "flavor" rather than "version", since "version"
might imply e.g. 1.53c or 1.53d or 2.2.0, whereas "flavor" less ambiguously
refers to e.g. ImageJ 1.x, ImageJ2, Fiji, Bio7, AstroImageJ, etc. See
https://imagej.net/software/imagej for a table of these.

This naming is used throughout the code, publications, tutorials, web
materials, etc.:

- The groupId of both ImageJ 1.x and ImageJ2 components is net.imagej.
- The GitHub organization of both ImageJ 1.x and ImageJ2 repositories is
imagej.
- The Java package prefix of ImageJ2 classes is net.imagej.*.
- The JAR files are named with "imagej-" prefix, e.g. "imagej-updater".
- ImageJ2 components are named e.g. "ImageJ Updater" (not "ImageJ2
Updater").
- The title bar of the plain ImageJ2 application is currently "ImageJ", not
"ImageJ2" -- although we may change this to make it more obvious when a
running ImageJ instance is the ImageJ2 flavor.
- Several publications, such as the ImageJ2 paper (
https://doi.org/10.1186/s12859-017-1934-z), refer to "ImageJ" as a project
encompassing either or both of ImageJ 1.x and ImageJ2. For example: "There
are two ImageJ components dedicated to maintaining backwards compatibility
with ImageJ 1.x."
- Communication on public lists and forums has always referred to the
ImageJ2 effort as "ImageJ development" and similar phrasing. For example:
"LOCI submitted a successful proposal to NIH to fund ImageJ development"
(from ImageJ2's original project announcement on the ImageJ list --
Bad URL Removed - see why - https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?A2=ind0912&L=IMAGEJ&D=0&P=81277).

In short: "ImageJ2 is ImageJ" -- a different flavor than the original
ImageJ, with distinct project goals and features, but still ImageJ.


On Tue, Jun 15, 2021 at 11:58 PM Wayne Rasband <[hidden email]> wrote:

> Hi Curtis,
>
> > On Jun 15, 2021, at 9:09 AM, Curtis Rueden <[hidden email]>
> wrote:
> >
> > Hi everyone,
> >
> > In response to this thread, I have done the following:
> >
> > * The front page (https://imagej.net/) now says "Welcome to the ImageJ
> > ecosystem" and shows a disambiguation box explaining about the two
> flavors
> > of ImageJ, ImageJ1 and ImageJ2, with links to more information.
>
> Thanks for making these changes. The new imagej.net front page is much
> better but I would prefer the two flavors to be ImageJ and ImageJ2. The
> Java version of NIH Image has been “ImageJ” for 24 years and I see no need
> to call it anything else. In any case, ImageJ 1.x is better than ImageJ1.
> There is no program named ImageJ1 but there is an ImageJ 1.53j (the current
> version).
>
> > * The downloads page (https://imagej.net/downloads) now clearly links to
> > the download pages of both Fiji and ImageJ1, with a sidebar explaining
> why
> > there is not yet a download for plain ImageJ2.
>
> This page is also much better but the download choices should be Fiji and
> ImageJ, or at least Fiji and ImageJ 1.x.
>
> > * On that same page, just below the download links, there is an
> expandable
> > box with the label "Need help deciding? Click here." that lists some
> bullet
> > points in favor of each system. As a software engineer, I dislike
> > marketing-style comparisons; my goal with this table was to sum up, for
> new
> > users, why you might want to use each tool. Contributions to these
> > respective bullet point lists are welcome, especially if you feel a major
> > strength of either ImageJ1 or ImageJ2 is missing from the table—please go
> > ahead and edit the wiki page directly.
>
> Here are four more ImageJ advantages:
>
>   1. It’s smaller, an 81 MB download versus 474 MB for Fiji.
>   2. It has a built in Java compiler.
>   3. There is a version that runs in Web browsers (https://ij.imjoy.io/).
>   4. There is a version that runs natively on m1 (arm64) Macs.
>
> I will try to edit the wiki page.
>
> > * I removed the "© ImageJ" from the imagej.net footer; it was left over
> > from the original theme. The license for the imagej.net website is CC BY
> > 3.0 (https://github.com/imagej/imagej.github.io/blob/main/LICENSE.txt).
>
> Thanks for removing the copyright notice. ImageJ is in the public domain,
> so it was inappropriate.
>
> > * I moved ImageJ2's top-level GitHub repository from
> > https://github.com/imagej/imagej to https://github.com/imagej/imagej2.
> This
> > hopefully helps clarify that imagej/imagej1 is the repository for
> ImageJ1,
> > and imagej/imagej2 is the repository for ImageJ2. We should not have any
> > repository at https://github.com/imagej/imagej because it would be
> > ambiguous. Relatedly, it would be nice to eliminate the imagej/ImageJA
> > repository, but I do not think it is technically feasible unless Wayne
> > changes the ImageJ1 release workflow.
>
> What are the workflow changes that would be needed to eliminate the
> ImageJA repository?
>
> -wayne
>

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

[Herbie]

Thanks Curtis,

for the proposed changes.

As the initiator of this thread, I'm a little late because of an not
insignificant personal celebration...

I'm not perfectly happy with the extent of the proposed changes in
terminology and how they are or will be reflected on the various websites.
(Here I refer to both of your replies on this list.)

_____________
"In short: 'ImageJ2 is ImageJ' -- a different flavor than the original
ImageJ, with distinct project goals and features, but still ImageJ."

ImageJ2 is definitely _not_ ImageJ.
You may state that ImageJ2 is planned to become an ImageJ _flavor_ or
_derivative_ but it is not and will never be ImageJ. "ImageJ" and "ImageJ
flavors" are different concepts.
ImageJ is the name of a software developed by Wayne Rasband, nothing else.
_____________
Here:
"- The title bar of the plain ImageJ2 application is currently 'ImageJ', not
'ImageJ2' -- although we may change this to make it more obvious when a
running ImageJ instance is the ImageJ2 flavor."

You really _should_ change it as soon as possible because, as you write,
ImageJ2 at best is or was planned to be a flavor or derivative of ImageJ.
_____________
"Several publications, such as the ImageJ2 paper
(https://doi.org/10.1186/s12859-017-1934-z), refer to 'ImageJ' as a project
encompassing either or both of ImageJ 1.x and ImageJ2."

The fact that a paper contains such statements doesn't imply they are
correct. I don't see Wayne as a co-author, consequently he could not
intervene...
_____________
"Community Partners" on the webpage <https://forum.image.sc> still lists
ImageJ with the yellow-greenish logo. This logo or icon doesn't apply to
ImageJ because ImageJ has an icon of its own.
The same holds for the explanatory text that opens when clicking on the very
link.
Both need to be changed immediately.

From the FAQ of "forum.image.sc":
"A Community Partner is an open-source software project or community
organization that uses this forum as a primary recommended discussion
channel."
This condition is _not_ met by "ImageJ" because it has its own and
recommended communication and discussion channel, namely this Mailing List
<https://imagej.nih.gov/ij/list.html> that already existed many years before
the Forum was established.
_____________
As a compromise, I'd like to propose to link the term/abbreviation "IJ" to
the yellow-greenish logo and to also use this term/abbreviation for the
umbrella of possible flavors or derivatives, i.e. as the generic term.

The term "ecosystem" for a functionally related group of software, although
meanwhile used in the sense of "Digital ecosystem"
<https://en.wikipedia.org/wiki/Digital_ecosystem>, appears being a bit off
or at least merely trendy.
I'd prefer and suggest "umbrella".

==============

In short:
Please leave the term "ImageJ" exclusively for the scientific image
processing software developed by Wayne Rasband.

It is good scientific practice to not use terms, introduced for results of
specific research, for differing results of endeavors of different authors.
Wayne Rasband introduced the term "ImageJ" for the result of his scientific
software development. He holds the naming priority.

The fact that ImageJ2 partly follows the line of "ImageJ" doesn't justify to
call it "ImageJ", or part of it, in the ecosystem/umbrella sense.

Why not name ImageJ2 completely differently? The name Fiji is a nice example
(it doesn't denote ImageJ).

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::

Curtis Rueden-2 wrote

> Hi everyone,
>
> Wayne and I discussed off-list, and agreed that ImageJ2 and the original
> ImageJ (a.k.a. ImageJ 1.x) are both official versions of ImageJ. In cases
> where the distinction matters, please refer to them respectively as
> "ImageJ2" and "ImageJ 1.x" (not ImageJ1). See the P.S. below for further
> details.
>
> I have updated the imagej.net website to remove as many usages of the term
> ImageJ1 as possible:
>
> https://github.com/imagej/imagej.github.io/commit/a3f228a66418e9e227ed1f472ff747528a4a8135
>
> In the coming days I will work on restoring the ImageJ wiki's project icon
> feature, so that each page can have an icon next to its title indicating
> its scope, with tooltip giving more information upon mouseover. So e.g.
> pages about ImageJ 1.x plugins will have the ImageJ 1.x logo, pages about
> ImageJ2 plugins will have the ImageJ2 logo, and pages about plugins
> bundled
> with Fiji will have the Fiji logo. (I may also implement support for pages
> belonging to multiple projects -- e.g. a Fiji plugin built on ImageJ2
> should probably show both logos.) Any other suggestions for clarifying
> these distinctions across the wiki are most welcome.
>
> Wayne Rasband wrote:
>> I will try to edit the wiki page.
>
> Looks good. Thank you!
>
>> Thanks for removing the copyright notice. ImageJ is in the public
>> domain, so it was inappropriate.
>
> Just to clarify: a copyright notice at the bottom of a webpage declares
> the
> copyright for the website content, not the copyright of any software being
> documented. The intent was never to declare any sort of copyright there
> relating to the ImageJ programs (neither ImageJ 1.x nor ImageJ2).
>
>> What are the workflow changes that would be needed to eliminate the
>> ImageJA repository?
>
> The page https://imagej.net/libs/imageja briefly describes why ImageJA
> still exists, and how changes to ImageJ flow from imagej/imagej1 to
> imagej/ImageJA to binary builds deployed to OSS Sonatype. The two relevant
> CI jobs are:
> * https://travis-ci.com/github/imagej/ij1-builds -- generates commits to
> ImageJA matching the ImageJ letter releases
> * https://travis-ci.org/github/imagej/ImageJA -- builds and deploys ij.jar
> in response to changes to ImageJA
>
> A better workflow would be to push changes to the ImageJ repository
> whenever you want, and use the SciJava release-version.sh script to cut
> letter releases, as described at https://imagej.net/develop/releasing. If
> you'd like to discuss it further, I can file an issue on GitHub with more
> information, so we don't splinter the discussion thread.
>
> Regards,
> Curtis
>
> P.S. Here is a summary of how the ImageJ projects have been named since
> 2010 when the ImageJ2 project was funded:
>
> * ImageJ2 is a new version of ImageJ, targeting a broader set of
> scenarios,
> and focused on scientific imaging.
> * As such, the term "ImageJ" can refer to ImageJ 1.x, ImageJ2, or both
> together.
> * The term "ImageJ components" refers to any or all software components
> (JAR files) in the imagej GitHub organization, with groupId net.imagej --
> for example:
>     - net.imagej:ij (ImageJ 1.x -- ij.* packages)
>     - net.imagej:imagej (ImageJ2 top-level project -- net.imagej.*
> packages)
>     - net.imagej:imagej-common (ImageJ Common -- net.imagej.* packages)
>     - net.imagej:imagej-updater (ImageJ Updater -- net.imagej.updater.*
> packages)
>     - net.imagej:imagej-ops (ImageJ Ops -- net.imagej.ops.* packages)
>   E.g. "ImageJ Common is a component of the ImageJ project, and part of
> ImageJ2, the redesigned version of ImageJ."
> * The program "Fiji" is a distribution of ImageJ (both ImageJ 1.x and
> ImageJ2 together).
> * The term "Fiji components" refers to software components (JAR files) in
> the fiji GitHub organization, with groupId sc.fiji -- e.g.
> sc.fiji:TrackMate_.
> * We often use the term "flavor" rather than "version", since "version"
> might imply e.g. 1.53c or 1.53d or 2.2.0, whereas "flavor" less
> ambiguously
> refers to e.g. ImageJ 1.x, ImageJ2, Fiji, Bio7, AstroImageJ, etc. See
> https://imagej.net/software/imagej for a table of these.
>
> This naming is used throughout the code, publications, tutorials, web
> materials, etc.:
>
> - The groupId of both ImageJ 1.x and ImageJ2 components is net.imagej.
> - The GitHub organization of both ImageJ 1.x and ImageJ2 repositories is
> imagej.
> - The Java package prefix of ImageJ2 classes is net.imagej.*.
> - The JAR files are named with "imagej-" prefix, e.g. "imagej-updater".
> - ImageJ2 components are named e.g. "ImageJ Updater" (not "ImageJ2
> Updater").
> - The title bar of the plain ImageJ2 application is currently "ImageJ",
> not
> "ImageJ2" -- although we may change this to make it more obvious when a
> running ImageJ instance is the ImageJ2 flavor.
> - Several publications, such as the ImageJ2 paper (
> https://doi.org/10.1186/s12859-017-1934-z), refer to "ImageJ" as a project
> encompassing either or both of ImageJ 1.x and ImageJ2. For example: "There
> are two ImageJ components dedicated to maintaining backwards compatibility
> with ImageJ 1.x."
> - Communication on public lists and forums has always referred to the
> ImageJ2 effort as "ImageJ development" and similar phrasing. For example:
> "LOCI submitted a successful proposal to NIH to fund ImageJ development"
> (from ImageJ2's original project announcement on the ImageJ list --
> Bad URL Removed - see why -
> https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?A2=ind0912&L=IMAGEJ&D=0&P=81277).
>
> In short: "ImageJ2 is ImageJ" -- a different flavor than the original
> ImageJ, with distinct project goals and features, but still ImageJ.
>
>
> On Tue, Jun 15, 2021 at 11:58 PM Wayne Rasband &lt;

> rasband@

> &gt; wrote:
>
>> Hi Curtis,
>>
>> > On Jun 15, 2021, at 9:09 AM, Curtis Rueden &lt;

> ctrueden.wisc@

> &gt;
>> wrote:
>> >
>> > Hi everyone,
>> >
>> > In response to this thread, I have done the following:
>> >
>> > * The front page (https://imagej.net/) now says "Welcome to the ImageJ
>> > ecosystem" and shows a disambiguation box explaining about the two
>> flavors
>> > of ImageJ, ImageJ1 and ImageJ2, with links to more information.
>>
>> Thanks for making these changes. The new imagej.net front page is much
>> better but I would prefer the two flavors to be ImageJ and ImageJ2. The
>> Java version of NIH Image has been “ImageJ” for 24 years and I see no
>> need
>> to call it anything else. In any case, ImageJ 1.x is better than ImageJ1.
>> There is no program named ImageJ1 but there is an ImageJ 1.53j (the
>> current
>> version).
>>
>> > * The downloads page (https://imagej.net/downloads) now clearly links
>> to
>> > the download pages of both Fiji and ImageJ1, with a sidebar explaining
>> why
>> > there is not yet a download for plain ImageJ2.
>>
>> This page is also much better but the download choices should be Fiji and
>> ImageJ, or at least Fiji and ImageJ 1.x.
>>
>> > * On that same page, just below the download links, there is an
>> expandable
>> > box with the label "Need help deciding? Click here." that lists some
>> bullet
>> > points in favor of each system. As a software engineer, I dislike
>> > marketing-style comparisons; my goal with this table was to sum up, for
>> new
>> > users, why you might want to use each tool. Contributions to these
>> > respective bullet point lists are welcome, especially if you feel a
>> major
>> > strength of either ImageJ1 or ImageJ2 is missing from the table—please
>> go
>> > ahead and edit the wiki page directly.
>>
>> Here are four more ImageJ advantages:
>>
>>   1. It’s smaller, an 81 MB download versus 474 MB for Fiji.
>>   2. It has a built in Java compiler.
>>   3. There is a version that runs in Web browsers (https://ij.imjoy.io/).
>>   4. There is a version that runs natively on m1 (arm64) Macs.
>>
>> I will try to edit the wiki page.
>>
>> > * I removed the "© ImageJ" from the imagej.net footer; it was left over
>> > from the original theme. The license for the imagej.net website is CC
>> BY
>> > 3.0 (https://github.com/imagej/imagej.github.io/blob/main/LICENSE.txt).
>>
>> Thanks for removing the copyright notice. ImageJ is in the public domain,
>> so it was inappropriate.
>>
>> > * I moved ImageJ2's top-level GitHub repository from
>> > https://github.com/imagej/imagej to https://github.com/imagej/imagej2.
>> This
>> > hopefully helps clarify that imagej/imagej1 is the repository for
>> ImageJ1,
>> > and imagej/imagej2 is the repository for ImageJ2. We should not have
>> any
>> > repository at https://github.com/imagej/imagej because it would be
>> > ambiguous. Relatedly, it would be nice to eliminate the imagej/ImageJA
>> > repository, but I do not think it is technically feasible unless Wayne
>> > changes the ImageJ1 release workflow.
>>
>> What are the workflow changes that would be needed to eliminate the
>> ImageJA repository?
>>
>> -wayne
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
Sent from: http://imagej.1557.x6.nabble.com/

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

[Wayne Rasband-2]

Thanks to Curtis, the https://imagej.net website now does a better job of distinguishing between the original version of ImageJ and ImageJ2 (Fiji), a new version with advanced capabilities. I am especially pleased to see the main page now refers to the original version as “ImageJ”, not “ImageJ1” or “ImageJ 1.x”.

The imagej.net website is hosted on GitHub Pages, which allows users to edit the pages. I was able to update the ImageJ page (https://imagej.net/software/imagej-1.x), the Downloads page (https://imagej.net/downloads) and the Contribute page (https://imagej.net/contribute/).

It also hosts the ImageJ downloads site (http://wsr.imagej.net), used by the Help>Examples and Help>Update ImageJ commands, the sample images (https://imagej.net/images/), used by the File>Open Samples command, as well as a mirror of https://imagej.nih.gov/ij/ (https://mirror.imagej.net).

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

[Herbie]

Greetings to all

interested in the subject's question.

It appears as if most of the before mentioned problems, or should I say
challenges, are now solved or coped with.

However, after a short period of correct display, the panel showing the
Community Partners on the Form presently appears in a strange and
obviously wrong way (see attached screen-shot).

I'm sure this perhaps final glitch will also be remedied.

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::
Am 18.06.21 um 20:43 schrieb Wayne Rasband:
> Thanks to Curtis, the https://imagej.net website now does a better job of distinguishing between the original version of ImageJ and ImageJ2 (Fiji), a new version with advanced capabilities. I am especially pleased to see the main page now refers to the original version as “ImageJ”, not “ImageJ1” or “ImageJ 1.x”.
>
> The imagej.net website is hosted on GitHub Pages, which allows users to edit the pages. I was able to update the ImageJ page (https://imagej.net/software/imagej-1.x), the Downloads page (https://imagej.net/downloads) and the Contribute page (https://imagej.net/contribute/).
>
> It also hosts the ImageJ downloads site (http://wsr.imagej.net), used by the Help>Examples and Help>Update ImageJ commands, the sample images (https://imagej.net/images/), used by the File>Open Samples command, as well as a mirror of https://imagej.nih.gov/ij/ (https://mirror.imagej.net).
>
> -wayne
> --

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