Hi Robert, I join Kareem on the documentation. One possibility is to add a the word “documentation” with a link to both docs after the presentation of the two packages in bullet points. Still regarding documentation, the documentation of HDF5_BLS_treat is also on the tutorial of HDF5_BLS. When I find time somewhere I’ll make a dedicated documentation for it (and a wiki) but as is, the readthedocs only documents the HDF5_BLS package and not the HDF5_BLS_treat. Aside from that, good to go also for me :) Best, Pierre Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria
On 6/9/25, at 08:29, Robert Prevedel via Software <software@biobrillouin.org> wrote:
Dear all,
thanks for everybody’s feedback - I’ve now prepared the documents for bioRxiv, please find them attached. I tried to unify nomenclature, links etc as much as possible. It might not be 100% consistent but I think this shouldn’t hold back the preprint.
In case you spot anything that’s really off let me know. Otherwise I plan to upload to bioRxiv some time tomorrow!
Have a nice weekend,
Robert -- Dr. Robert Prevedel Group Leader and Senior Scientist Cell Biology and Biophysics Unit European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg, Germany
Phone: +49 6221 387-8722 Email: robert.prevedel@embl.de http://www.prevedel.embl.de
<Brillouin file format paper final bioRxiv.pdf> <Brillouin file format paper final SI bioRxiv.docx> <Brillouin file format paper final SI bioRxiv.pdf> <Brillouin file format paper final bioRxiv.docx>
On 05.09.2025, at 13:30, Sal La Cavera Iii via Software <software@biobrillouin.org> wrote:
Hi all,
Just made a pass through the latest 'final draft' version of the manuscript. It looks really good and I reckon it's basically ready for preprint stage. I'll defer to Carlo/Pierre on whether the software is ready for deployment to complement the preprint release. From my end there are 2 very minor outstanding items to solve re: brimconverter and brimfile / hdf5_bls that I'm working on with Carlo/Pierre, but these shouldn't hold back the release I think. (and also brimconverter is officially implemented into the brimfile library, thanks for the help on this Carlo!).
It may be tough to meet next week (the proposed Thursday meeting) because I'll be visiting my parents, but I can still support offline when needed. But again happy for the preprint to go live Monday.
Also, the BioBrill newsletter draft + proposal for a talk/roundtable at BioBrill in Nov sound great. The only stipulation I would make is that whoever presents the project to the audience should have to wear a black turtle neck sweater with wire rim glasses :)
Best,
Sal
--------------------------------------------------------------- Salvatore La Cavera III Royal Academy of Engineering Research Fellow Nottingham Research Fellow Optics and Photonics Group University of Nottingham Email: salvatore.lacaveraiii@nottingham.ac.uk <mailto:salvatore.lacaveraiii@nottingham.ac.uk> ORCID iD: 0000-0003-0210-3102 <image.png> <https://outlook.office.com/bookwithme/user/6a3f960a8e89429cb6fc693c01d10119@...> Book a Coffee and Research chat with me! From: Kareem Elsayad via Software <software@biobrillouin.org <mailto:software@biobrillouin.org>> Sent: 05 September 2025 10:15 To: Software Mailing list <software@biobrillouin.org <mailto:software@biobrillouin.org>> Subject: [Software] Re: Paper preprint
Thanks Robert,
Fine by me: reading through last version already sounded quite complete/ready (as for completeness of codes, I cannot comment). …also see no harm as can always submit slightly modified version to journal if we find small things we want to change still, and when/if through ofcourse upload new one on arxiv…
All the best, Kareem
From: Robert Prevedel via Software <software@biobrillouin.org <mailto:software@biobrillouin.org>> Reply to: Robert Prevedel <prevedel@embl.de <mailto:prevedel@embl.de>> Date: Friday, 5. September 2025 at 09:11 To: Software Mailing list <software@biobrillouin.org <mailto:software@biobrillouin.org>> Subject: [Software] Paper preprint
Dear all,
as I understood, Pierre would appreciate a preprint being out before Sept. 10 for his grant application, and likelywise I’d be happy to see cite it in mine.
This would mean we’d need to upload to e.g. bioRxiv by Monday evening the latest. Is everyone fine with this plan and ok given their state of code etc.? Also, please alert me of any last changes to the paper online in case you do any.
Best,
Robert -- Dr. Robert Prevedel Group Leader and Senior Scientist Cell Biology and Biophysics Unit European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg, Germany
Phone: +49 6221 387-8722 Email: robert.prevedel@embl.de <mailto:robert.prevedel@embl.de> http://www.prevedel.embl.de <http://www.prevedel.embl.de/>
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