Formal policy for project to be a software partner



Definitely yes to this one. Notice at the bottom of any topic email notification, there is a message “Visit Topic or reply to this email to respond.”

Yes, Discourse supports this. It even (optionally) supports starting topics from email addresses who are not already users, via something called “staged users”. However, these features would need to be enabled in the settings. It looks like the basic toggle is called “email in” and default minimum trust level is 2. But at a quick glance, I suspect configuring everything properly may be more involved than just that checkbox. I recall that @thewtex told me it was quite tricky to get all these email-related features working as desired for the ITK forum.

Personally, I would be reluctant to enable starting new topics via email because I am concerned it could bring along issues of increased spam, and therefore moderation effort. However, if you feel the potential burden would be worth it to placate the email-centric people, and want to give it a try, then please feel free to read up on how it works in more detail and do some experiments with it. I promoted you to admin just now, so there should be no technical obstacles to you doing so.


First, hats off to @ctrueden for making this happen! It is a great idea, and it did not come to fruition without quite a bit of effort.

For the ITK’s community’s migration to Discourse, mailing list behavior was a must for many in the community. And while it is not completely perfect, i.e. a user cannot specify that they want plain-text email and quotes are sometimes funky, most folks who gave it a chance found it to be a practical mailing list replacement. Here are the instructions to use Discourse as a mailing list for ITK.

I added a link to on the ITK Discourse Welcome Topic. Hopefully, ITK can officially join as an community partner at some point. We will visit this in about half a year to a year. ITK is currently migrating to GitHub, and this should be finished before other community infrastructure changes. ITK’s migration to Discourse is also relatively recent, so it is a good idea to let the dust settle before making another major change.

There are a number of other changes we made to ITK’s Discourse configuration – it would not hurt to make those changes here, too :wink:

  • Check email time window mins
  • Increase newuser max images and newuser max attachments
  • Enable fixed category positions and order categories
  • Remove facebook from share links
  • Add Announcements category to default categories watching
  • Pin a Using Discourse as a mailing list topic in Uncategorized
  • Finalize the “getting started” guide for Discourse, and link to it in the welcome banner
  • Change “like” button icon from a heart to thumbs up
  • Tweak email contents (retain %{respond_instructions} )
  • Settings -> top menu -> “categories” on left (so it is first)
  • Set min trust level to create tag to 1
  • Increase title max word length to 150
  • Add * to the list of authorized extensions
  • Increase newuser_spam_host_threshold from 3 to 10
  • To allowed iframes add,, (for posts like this)


@ctrueden well, that’s why I said we should only allow posts from registered users. I think that should be quite effective at combating spam…?

@thewtex doesn’t mention spam issues which makes me think they didn’t encounter any. =)

@thewtex thanks so much for all that info, it’s very very useful!


I hope it helps!

Some additional settings:

  • email time window mins: 1
  • email posts context: 0
  • email subject: %{site_name} %{optional_pm}%{topic_title}
  • email prefix: [ITK]
  • unsubscribe via email footer: checked

We have not received any spam, but I believe we are using a good spam filtering service for which Kitware has a subscription.

Registration to participate via GitHub and Google login lowers the barrier to entry substantially relative to mailing list subscriptions. Also, many younger community members do not know how to subscribe to a mailing (sadly).


Thank you for making this possible! This type of initiative is very useful for anyone working within the bio-imaging community.

Regarding “A) the organization links to the forum in its documentation regarding how users should seek support and/or discussion”
Some commercial software includes dedicated technical and application support. In those cases (at least some of) the users will likely contact the company directly to get tech and app support. Is it OK to leave it up to the user to decide where he/she posts their question? If the user decides to post publicly the answer could also be public. But if the question is posted privately to the company then the reply would also be private. Thoughts?

A couple of other questions which may help other companies join this effort:

  1. can we add a note indicating that using this forum will always remain public and free of charge?
  2. can companies continue to have their own newsletters or similar?
  3. is there any plan to have advertising (personally I am against the idea) spots on this forum?

Many thanks!


While it is perfectly acceptable that solutions involving commercial software are discussed on this forum, I’d like to question if closed-source software projects and companies can become a community partner of the forum: one of the aims of this forum is to foster independent learning, see here:

and from the forum guidelines:

An open source process enables this sort of learning thanks to its accessibility, transparency and reproducibility.

And finally, one of the sentences from that linked page on the ImageJ wiki:

In contrast, closed source software presents a barrier to open research, because the implementation details of algorithms cannot be freely modified or even necessarily verified.

What do others think about this?

Regarding the other questions you asked:

This is already specified in the Terms of Service:

User contributions are licensed under a Creative Commons Zero (public domain) license

There’s no plan, and – as long as funding is secured – I very much hope there will never be commercial advertising on this forum.


Thank you - I understand. While I do appreciate the difference between open and closed source software I also think there a significant value in having a bio image analysis community that includes all parts. In line with:

That said, this great forum was originally created by and for open source projects. Thus, it would be a significant (or even odd) step to embrace closed source projects in the same forum. On the other hand, keeping closed-source projects out limits the potential positive impact of this forum.

One (simple) solution would be to make it obvious to the users which are the open vs the closed source projects. e.g. by adding a badge to the logo of the project?



To make it clear, perhaps the statement could be tweaked to

Discussion of any and all scientific image software tools is warmly welcomed, but only open source tools using the forum as a primary recommended discussion channel will be included in the navigation bar.


Somebody has to say it first… so here it goes: I would not like to have closed source or commercial products featured in this forum.
It would be quite unfair to the grant bodies that fund the many projects hosted here, to administrators and to moderators who put their work for free.
There are plenty of options for companies to support their products and users base.


Any chance we could discuss this?

The interplay between commercial and academic software is getting stronger and stronger nowadays. For instance Imaris ships a connector to Fiji and implemented their version of S, Preibish algorithms, Yokogawa ships Fiji directly, Arrivis took inspiration from iLastik, ImageJ2 has bridges to MATLAB,

However - most of the time - this is a unilateral action. There is little discussions between the two parts (with good exceptions though). It feels like we are all having a great time around a nice table, but some guests are missing. If we include commercial partners in this forum, this will bring them closer to our community and give them a voice and also ears there.

Also, with the merge, this forum is focusing more and more on problem solving. We cannot cut ourselves from a large part of the solutions. Realistic analysis workflows involve several software components, and some of them commercial ones, that deserves being discussed here.

Of course, we must also try to predict what could go wrong. For instance:

  • Being used as a commercial advertisement platform.
  • Arguing - sometimes vividly - around different solutions not based on a scientific rationale. Think of trolls.
  • Posts like “This is too expensive for us”.

But I don’t see these 3 points as being fixed by excluding commercial partners.

We had a good experience in NEUBIAS by offering a platform to a commercial platform to teach, based on their commercial solution. And it went fine. The courses focused on doing Science and it did not turn into advertisement at all. We even had a good discussion on the limitations of the solution. We could have this here too.


Hi all

I think it would be very beneficial to the community if users, and developers of commercial software are encouraged to post. Though I agree, it seems reasonable that only open source tools should be in the navigation bar.

@tinevez just made a very good post. I don’t have much to add, however I will say by excluding commercial partners, you may inadvertently make science less open. For example if we say that commercial companies can simply use their own support channels, then those commercial solutions will be discussed in a small private bubble.

If we encourage commercial companies to post here, then it brings the discussion out into the open.


Yes, posting and featuring are two very different things. I expressed my feelings about featuring.


It is important to keep commercial well-defined as “making a profit.” There are many businesses, especially in modern times, that work with or produce open source software. Today, many would even consider Microsoft an open source software company. And, academic institutions also have a business model. The ability to make a profit helps with the sustainability and overall health of our community. So, commercial partners should be welcome.

But, closed source software conflicts with the “science” and “learning” goals of the forum. “Problem solving” is related, but it is not the same; as suggested by @bnorthan and @gabriel ,it seems reasonable to welcome posts that may require closed source software, but not have them featured in the navigation bar.


I second Gabriel,

mostly for two reasons:

  1. Shall volunteers do the hotline work for commercial companies?
  2. What about the competence of us volunteers concerning commercial software?

If companies build bridges to open/free software, they are to handle any related problems themselves: It’s their decision and their business.

If academic institutions become partially commercial, then they have to act accordingly and provide assistance/help on a commercial level.




I would expect that the tech and app support teams from different companies would be the ones responding. That said, on a number of occasions I have seen Imaris users provide expert support to other users, via that product’s discussion forum. Not sure that should be inhibited as it seems to be good for increasing transparency and advancing everyone’s work.

Some users are as knowledgeable or even more knowledgeable than the team members doing tech and app support. So, while I think the responsibility lies with the companies to provide support in a timely manner I dont think the wider community should be stopped if they feel they can help.

Totally agree, the responsibility for support is with the companies / project owners.


Sorry, but I can’t agree with what you replied to 1. and 2.

I would expect that the tech and app support teams from different companies would be the ones responding.

My experience is they won’t for a long period of time because it means less work to wait until a volunteer chimes in. Only if there is no or wrong advice they may respond.

Again: No commercial products on this Forum!

Some users are as knowledgeable or even more knowledgeable than the team members […]

With this opinion you assume that there are many users that can afford commercial products and are experienced with their use. However, this Forum is mainly meant for those who use open source and free software.

Again: No commercial products on this Forum!




Dear Forum
(Thank you for the input Herbie)

It is certainly possible for this to happen. It depends on where the question is posted for example (on the company forum or on another forum). It will also be influenced by whether the user posting is a known user with a valid tech / app support - those naturally get priority. There are several other factors.
My original comment was specific about the company I currently work with - i.e. the one I can control to ensure we would follow up on tech/app support requests on this forum.

When visiting microscopy core facilities and individuals labs around the world I see they typically use several pieces of software from free and open source all the way to commercial and closed source to complete a pipeline. Many tools (free, commercial, open and closed) aim to provide users a complete workflow. The reality is users select a few tools and string them together to complete their work (often including one ore more commercial tools along with FIJI apps and other great tools).

As I mentioned above, this forum was created by and for open source tools. At the start of this thread / discussion it looked like the forum was considering to include other tools. Also, on twitter (where I originally saw the news) it looked very much like it was an effort to bring all tools under one roof (not just the the open source ones). see for example: or more generally,

The more vocal users on this thread have made it clear that the forum should be for open source tools only (commercial or not is another question). Naturally, I respect those opinions - everyone in the community has a voice. I will continue to do my part to make the wider bio image analysis community a stronger / better / more impact-full one.

All the best


Hi all,

I really hope that this discussion leads to balanced opinions on both sides.

I really do not think that any company sees this forum as a replacement for their own support etc. At least that is true for the one I am working for.
But as already explained most people use free and commercial tools, closed and open source.
So if someone has a question and somebody suggests a solution that involves a commercial solution, why is this a problem? And even if it would be closed source it is still up to the user to decide which software to use.
And the fact that companies make money is not something bad, because money for research and grants must finally come from somewhere, isn’t?

So please set up clear rules what companies can post here. And certainly I encourage discussions about used algorithms etc. But that does not automatically mean that every company should publish their complete source code. Or is this expected?

Sebi (from Zeiss)


To reiterate @thewtex’s lost point: we should certainly distinguish between commercial/for-profit, and closed source. ITK/Kitware is a great example of a for-profit company benefiting from and giving back to the open source community. In contrast, Zeiss (sorry to pick, Sebi) recently released Intellisis, a blatant clone of Ilastik, while making zero contributions back (as far as I can tell, would be delighted to be corrected).

I’m sure many in this forum have been frustrated with the difficulty of getting funding for open source development, while at the same time the very departments that employ them spend tens or even hundreds of thousands per year on licenses for closed source software.

In my opinion, this forum should be used to promote open tools, and thus lift all such tools. (And promote their interoperability.) This is not a strong opinion, and I’m happy to see the alternative side of everyone getting along. It absolutely doesn’t have to be a political decision or statement. But I would prefer if it were.



you don not have be sorry to pick the example of Intellesis from Zeiss, since I like to have an open discussion with people that disagree with my view.

But to be honest I do not think it is fair to call this software module a blatant clone, without knowing all the details of that tool.

  • it uses Python 3, Dask, Scikt-learn, Tensorflow and … which is all open source
  • in the process of developing it we reported a few bugs to dask that got fixed. Not much, but not nothing …
  • we make no secret about what we do in terms of algorithms
  • it uses a completely different way to handle multi-dimensional datasets compared to other tools
  • this software is all about integration in the existing measurment framework which others tools obviously cannot offer
  • And there a many other differences in the details

Just because it does pixel classification it is not a clone of ilastik. This is way to simplistic. Is every software that does pixel classification a clone of ilastik or in case of counting cells or stitching a clone of Fiji?

If that would be true many tools in the open source and free software world are also just clones of something developed by tax-payers money that could have been spend on something else. But I really like the diversity of tools and the option to choose what works best for me.

Seriously there are tons of tools in all areas that do similar things using partly the same ideas? Are all those useless and juts “clones” of someone favorite solution? Certainly not.

All those things were requsted by our customers to solve their issues with existing tools for their applications and workflows. Such tools are not developed to create a “clone” of an already existing solution but because their is a real need for that.
Moreover Zeiss does support especially Bio-Formats (it is a paid add-on of ZEN where licences fees have to be paid to the creators of Bio-Formats) and is involed in many research projects. Of course at some point as a company it has to earn money.

So what woukld be your idea of a real contribution that would allow a company to develop a tools that use a basic ideas that is already implemented somewhere?