Formal policy for project to be a software partner



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?


Hi @jni and @sebi06

I liked both your replies because I think these are the types of conversations that I think should be on this forum. Having an open conversation about the strengths and weaknesses of tools and development philosophies is always good.

As a side question did Zeiss ever consider developing open source tools?? Did anybody look closely at the economics of this?? How much revenue does the software generate as compared to hardware? Perhaps a difficult question to answer…

@thewtex I’m curious for your input on this as well. Are you aware of any analysis of open source vs. closed source business models for hardware companies?? I realize that is a pretty general question, but still curious.


Yes, there are plenty of open source software business models.

  • A hardware company selling sophisticated equipment can sell the hardware and provide supporting software open source. It is even possible to have open source hardware. Here is a nice, recent review of Emerging Business Models for Open Source Hardware.
  • Infrastructure services can be provided for open source software, providing the necessary hardware, software maintenance, and software integration. As imaging moves to the web, there are more opportunities here.
  • Companies, e.g. Red Hat, can sell support subscriptions for open source software.
  • Collaborative consulting services around open source software expertise is possible, e.g. Kitware.
  • Education and training services around open source software can be provided for a fee, e.g. universities, on-site training, online courses.

Closed source licensing models are often more profitable in the short term; in the long term, the cost, quality, flexibility, and capability of open source software wins out. We have seen this in microscopy with Fiji, which many scientists now simply prefer over closed source alternatives. We have seen this with Microsoft, which was extremely profitable in the 20th century with a closed source business model and actively hostile towards open source software, but it the 21st century it has been forced into an open source business model, i.e. Azure cloud computing services.

But, I hope this forum is agnostic to making money.

I would like to see a focus on imaging, science, and computing. Closed source software is sometimes required for current imaging workflows. However, closed source software does not allow inspection of the algorithms involved, extending the software for new research purposes, and sharing that software with other researchers so they can reproduce and understand the work. Open source software is required to reproduce and understand an experiment – it is necessary to do actual science.

To help strengthen the clarity of our purpose, we could

Enable open science and reproducible research.


Foster not only scientific independent thinking, but just as importantly, independent learning. We want to not only teach people how to fish, but teach them how to learn.

as stated in the ImageJ Wiki and previously emphasized by @imagejan.


Those are good arguments, but in reality life is not that simple. In microscopy i really do not see many of those open-source buisiness models that are commercially sucessful (yet?). That might change but currently at least one reason is that many research institutions are not willing or are not allowd to pay for service and infrastructure.

It rather encountered many times the issue that the idea of “free” software but paid service, maintainence and infrastructure was rejecteted from the resarch institutions, because the way grants etc mostly work today only allows for one-time payments.

Regarding the idea of providing infrastructure for open source computing it might be worth checking out (by ZEISS), which is a Docker and Kubernetes based image and data analysis platform that allows everybody to use their own code and tools.

And I have to make an additional remark here. We all love microscopy and image analysis (at least I do) and for years I had the assumption that most people using those techniques for their science think the same way, but reality is differnent. What many people want are just tools that get the job done. They do not have the time or the skills or the will to do a deep dive inside used techniques and algorithms on their open source tools or commercial tools.

As an example, how many people using a threshold or stitching (not speaking of things like DCV etc.) actually did check the used implementation inside their favourite open-source tool? In theorry everybody could do it but in reality most people just trust those tools and use it the same way they would use a commercial tool, where they cannot check out the source-code easily. People here on the forum are in average much more on the expert side of life than “average users”. For most of them the idea of checking the (open source) code is something which sounds cool, but will be rather unrealistic for many (good) reasons.

So did I understand it correctly that the main issue is not commercial or free, but closed-source or open-source, because every scientist must be able to “check” the used software in case of … ?


So did I understand it correctly that the main issue is not commercial or free, but closed-source or open-source, because every scientist must be able to “check” the used software in case of … ?

It depends on whom you ask…

I wrote (for good reasons):

No commercial products on this Forum!

Please read the whole thread!





i did read the complete thread, but it leaves many open questions. Much more than it answers, because some arguments ignore real life facts and over-simplify things.


i did read the complete thread […]

But you seem to have not considered my plea.

[…] some arguments ignore real life facts and over-simplify things.




Maintenance and infrastructure contracts are difficult to obtain from research institutions.

Practical approaches to work with research institutions:

  • Charge the actual cost of the hardware as part of the purchase and support contracts. I.e. do not require hidden software license fees to make the hardware useful.
  • Collaborate with grant PIs during the proposal period. Carving out funds later is often not feasible.

This looks cool.

The reality is that many people find the closed source tools limited and broken. And there is nothing they can do about it. Furthermore, when they want to re-analyze their data a year or two down the line, the data, which they may have spent have a decade of hard work to produce, is effectively lost because licensing funds are no longer available or the vendor simply decided to stop maintaining the closed source software. These are the real-life facts.

It happens often. Recently, in this thread, an attempt was made to compare Intellesis to Ilastik. It is not possible to have a solid understanding without the Intellesis source code. How, exactly, do they differ? How should we consider results created by the different algorithms and implementations?


Especially when it comes to a tool like Intellesis feel free to talk to me about details since I am in charge of this software.

So far just the statement was made that this is just cloning ikastik, which is not really the case. Yes it uses partly the same python modules but calling this a clone is a bit to harsh.

And this tool is never advertised claiming it has magic algorithms. It explicitly uses proven and estabshed open source libraries and does focus on UI, data handling and integration into ZEN measurement pipelines.

So it is a hybrid between both worlds. So let me know if you expect detailed info about such a tool here in this forum. Of yes I will do my best despite working for commercial company.

If this is wanted because its is commercial, this is also fine with me.