Formal policy for project to be a software partner



Hi, the point is not how many people do actually check the code, but that the process is transparent and that it can be done (and so it happens that checking is very often done). Many pairs of eyes see more than one pair. That is how many bugs are found, code is questioned and bugs are fixed, in my experience, way faster than commercial software that I have used.
One could use the same example and wonder how many bugs are there in software that nobody can tell what it does. Or whether bugs are too complicated or costly to fix, being left in a waiting list without notification.


Hi @gabriel

I agree with you completely that some commercial companies let bugs and issues lie waiting because it’s not profitable to fix them. However that’s all the more reason to welcome commercial companies.

While some bugs are found by examining the code, many (perhaps more) bugs are found by very carefully examining and discussing results and output images. If a user of a commercial product has a concern, they can post the images on this forum and get feedback from experts in image processing. If there is an issue, people can suggest open source approaches that may handle the problem. In turn the commercial company will either fix the problem quickly, or get bad publicity.

My suspicion is that the only commercial companies who will actively post here, are those who already have very good support, scientifically rigorous testing, and responsive bug fixing. In turn these are probably the companies that would be most receptive to some of the business models @thewtex has suggested. So it seems to me allowing such companies to post will lead to a positive cross-pollination of ideas and knowledge.


Let’s hope that the cross-pollination doesn’t turn out being a cross-pollution!

Brian your statements are full of hope and subjunctives.

We will see pollution by a great number of posts that are of the type:
How can I perform abc with xyz?

Where abc is an image processing problem and xyz is a commercial software that only a small number of the present Forum members sufficiently knows.

A consequence is that the Forum becomes clutterred and perhaps later may become increasingly visited by competent users (and makers) of commercial software.

Do we really want an extension to this clientel? I definitely don’t want to see it.

And finally, as Curtis has pointed out: Presently, companies that run their own help and support Forums are not considered being software partners of this Forum.




There is a lot to answer to here but I don’t want to nitpick so I’ll answer what I think are the two main questions from @sebi06:

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?

Well, you mentioned that you use Dask. Bug reports are useful, but since you are (presumably) making a decent profit out of Dask, perhaps you should devote resources to fixing these bugs yourselves.

Perhaps some percentage of the company profits should be donated to NumFOCUS or the Python Software Foundation so that the open source tools that you depend on can be better supported.

But, most of all, it would be nice if Zeiss open sourced Python packages for reading and writing .czi files, as just one small example. Or tools to integrate ZEN and Fiji/Python workflows. (Ditto, of course, for Leica, FEI, etc.)

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 … ?

Not every scientist will do so, this is true. But expert helpers will very often do this to understand what a particular bit of software is doing. The details matter a lot when trying to improve performance on a particular dataset. In other words, closing the source code is, at the detailed level, indeed “making a secret” of the algorithms you use.

I’m not ascribing maliciousness to this, just saying that the outcome is a real frustration for expert users, who often play in the 10% of cases where predefined workflows break in subtle ways, not in the 90% of “easy” cases.

As to business models, I am of course not a business expert. I can only say that when my institute comes to buy a new instrument, if a company charged a bit more for hardware but then did all of their software as open source tools that work nicely with the existing ecosystem, they would have a very persistent advocate in me. I imagine that I am not alone in this view.


Thx for your answers which i really appreciate.

We already haven a beta version if a python wrapper of our open-source libCZI, which can be hopefullz released soon.

Reporting a bug is one thing but being able (time and skillwise) to fix it is something different despite the fact somthing is open-source.

And increasing the hardware price by Holding the costs for the software is tricky. How should that work for software only? Most big software platforms a microcope vendors are much, much more than just hardware control.

And i want to point out again, that at least i never had the idea to use this forum for commercial support. I just was curious to find out what is allowed in cases of questions posted here that have to do with commercial tools or etc.


And i want to point out again, that at least i never had the idea to use this forum for commercial support.

What your ideas are and what actually will happen are completely different affairs.
If a user struggles s/he will search for help wherever possible and a Forum is independent of working hours, time zones, availability of a company’s experts, etc.

I must admit that now, after some days of fused Forums, I still don’t understand what CellProfiler has in common with ImageJ, except that ImageJ can be used for similar purposes. In fact, both systems are extremely different in their architectures and goals and I can’t see a direct software link between both. While ImageJ is quite universal, concerning the scope of applications, CellProfiler, as the name suggests, is more specialized. Both systems have their clientel and are justified but I would much prefer if they had their own Forums.

There must be a reason for getting bigger Forums that I presently don’t fully understand from a technical point of view …




Thanks to everyone for the vibrant discussion so far. I am really excited that we are having this conversation!


Speaking as one of the founders of this forum: we (the teams at LOCI and Broad) did discuss how commercial software would fit into the combined forum. Our intent is that discussion of commercial software, both open source and closed source, is welcome here.

Based on this conversation, I have expanded the relevant FAQ entry as follows:

And I have revised the FAQ entry “What is the forum’s mission?” as follows:

It is important to distinguish between embracing discussions of closed-source software vs. allowing closed-source community partners. My concerns regarding the latter have been expressed eloquently by @thewtex:

I feel an ethical obligation to structure this forum to promote open and reproducible science, which in this context entails open source.

It is also important to realize that open source alone is not enough. No software is perfect. Software may be buggy, poorly maintained, impenetrably complex, difficult to build, statistically unsound, produce irreproducible results… and still be open source. Furthermore: “Making something open isn’t a simple check box or button—it takes work, money, and time. Often those pushing for open access aren’t the ones who will have to implement it.” [source].

It is very challenging to write good software, and very challenging to pursue and communicate good science, even without any intentional secrets. We should do whatever we can to fight the replication crisis and enable science that is not only reproducible, but extensible.

As such, I personally do not support closed-source software projects being featured in the top-level navigation bar. But it would be great to see counterpoints argued here. It could also be possible to highlight the most useful and/or popular closed-source software projects in some other way—e.g. an expandable navigation drawer? Tag icons? Other ideas?


I personally would also not want any commercial tools at the top-level. I just want to be sure that in case somebody asks X and somebody (from a company or not does not matter) answer and suggests to use commercial tool Y, it would be OK to do so.
And of course people can point out that Y is closed-source etc. and therefore should not be used or ask for clarification.

I am well aware of the issues with closed-source software but som lot of e people inside the imaging community vastly underestimate to real costs and IP-releated issues with developing software and how hard the competition is.

So most IP departments and controlling will only give you money for development if you can prove that competitors can not easily copy it…
Believe me, those discussion can be very tricky. I know what I am talking about.