Project Migration to the DC-Analysis organization

[paulmueller]

I have decided to fork Shape-Out and continue its development at the more neutral DC-analysis GitHub Organization. The purpose of this issue is to communicate this fact to the community, transparently state the motivation for the migration, and answer any questions that might arise.

Motivation

Shape-Out originated at the TU Dresden, supported by Zellmechanik Dresden GmbH who gave Shape-Out its name and branding. Note that in the past years, I worked on Shape-Out as part of my contract at the Max Planck Institute for the Science of Light (a publicly funded organization in Germany), with my colleagues there, and without support by Zellmechanik.

I am a Cofounder of Rivercyte GmbH, a company that aims to establish deformability cytometry (DC) in the medical field. As Rivercyte maintains .rtdc file format compatibility, Shape-Out can also be used with their data, making Shape-Out a general analysis tool for DC. Due to obvious marketing reasons, Rivercyte has given a rebranded version "CytoPlot" to its users.

In general, there is no legal issue with the current situation. However, developing open source software as a community is always difficult when the branding of the software remains with a commercial entity. Even more so when said company does not contribute to the development of the software for years. Therefore, I believe that separating the development of Shape-Out from Zellmechanik is the best course of action.

Questions and Answers

To clarify things, I would like to answer a few questions that I thought of.

1. Shape-Out is a brand name. Will you rename it? Yes, the plan is to rebrand it under a company-neutral name in the DC-analysis organization. The new name is yet to be determined.
2. How can Zellmechanik keep marketing the software as Shape-Out? I would recommend using the scripts that Rivercyte used to rebrand Shape-Out (https://github.com/Rivercyte/CytoPlot/). Rivercyte will use the same approach, so Zellmechanik can in principle copy this approach and maintain their Shape-Out branding.
3. How will the transition happen? I plan to fork Shape-Out, copy all issues to the fork, and just continue development there. Then, Shape-Out users can either be notified about the change or Zellmechanik implements a workflow to keep Shape-Out up-to-date.
4. How am I supposed to cite the new software in a scientific publication? The citation scheme should be the same as described in the Shape-Out docs. To keep recognition rates high, I would add the term (formerly Shape-Out) in future publications.

Please don't hesitate to reply here (preferred) or via PM to clarify any points I missed.

@chrherold @maikherbig @MartaUrb @mkraete @phidahl @PinkShnack @RaghavaAlajangi

[chrherold]

Hi Paul,

I tried 5 versions of this and none of it was readable. So, I try again and hope to get the petty comment out of the way in the beginning: An “obvious marketing problem" only arises, if there are more copy and paste issues than just with open-source code.

On a factual basis I want to add this context to the history of ShapeOut:

Shape-Out originated from the founding process of ZELLMECHANIK DRESDEN GmbH at TU Dresden. Major developments of this project were directly funded by ZELLMECHANIK DRESDEN starting shortly after establishing the company in 2015 and ZELLMECHANIK DRESDEN also purchased the IP rights for RT-DC explicitly including ShapeOut from TUD – all of this is why it is branded as it is.

ZELLMECHANIK DRESDEN over the years funded maintenance and solely initiated and carried out the upgrade to Shape-Out2. The general workflow and GUI design still in place today was developed by people paid by ZELLMECHANIK DRESDEN for this purpose.

When you continue the development as a “neutral” project, effectively shedding the ZELLMECHANIK DRESDEN contributions by leaving our branding, we would like to request a proper and prominent acknowledgement of those past contributions in the copyright and authorship statements of the migrated software. If the new software is (and remains) compatible for users of our products, it would be another tool they can be directed at, make use of, and potentially contribute to. I doubt rebranding adds anything there.

We will have to decide how we continue development directions with ShapeOut and should probably transfer all responsibilities of this GitHub project to the company. We should also discuss how we properly acknowledge your past contributions to ShapeOut moving on.

Paul, we would like to thank you very much for your efforts on this software over the years! It has been very enjoyable and it has come quite a very long way for the essentially one-man-coding-show it was.

Liebe Grüße,
Christoph