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 [cid:80552fb6-313a-4f77-8fd5-d1c89f5d58a4]<https://outlook.office.com/bookwithme/user/6a3f960a8e89429cb6fc693c01d10119@...> Book a Coffee and Research chat with me! ________________________________ From: Kareem Elsayad via Software <software@biobrillouin.org> Sent: 05 September 2025 10:15 To: Software Mailing list <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> Reply to: Robert Prevedel <prevedel@embl.de> Date: Friday, 5. September 2025 at 09:11 To: Software Mailing list <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 http://www.prevedel.embl.de This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

Thanks Robert - looks great! Three small observations/suggestions: Think it would be good to cite Jitao’s Nat Protocols – quite fitting (maybe somewhere where we mention its finding broader applications (e.g. end of first or second paragraph) It might (just idea) be good to mention that we also provide extensive documentation. This is ofcourse clear from looking at Sup Mat, but could be explicitly mentioned in half sentence form in main text as selling point (just idea, not essential) DHO probably needs to be spelled out. Since only occurs once also no need for acronym. Aside from that, good to go from my side! 😊 Kareem From: Robert Prevedel via Software <software@biobrillouin.org> Reply to: Robert Prevedel <prevedel@embl.de> Date: Saturday, 6. September 2025 at 08:30 To: Software Mailing list <software@biobrillouin.org> Subject: [EXTERN] [Software] Re: Paper preprint 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 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 ORCID iD: 0000-0003-0210-3102 <image.png>Book a Coffee and Research chat with me! From: Kareem Elsayad via Software <software@biobrillouin.org> Sent: 05 September 2025 10:15 To: Software Mailing list <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> Reply to: Robert Prevedel <prevedel@embl.de> Date: Friday, 5. September 2025 at 09:11 To: Software Mailing list <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 http://www.prevedel.embl.de This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law. _______________________________________________ Software mailing list -- software@biobrillouin.org To unsubscribe send an email to software-leave@biobrillouin.org _______________________________________________ Software mailing list -- software@biobrillouin.org To unsubscribe send an email to software-leave@biobrillouin.org

Hi Robert, Only a couple very minor punctuation edits if you haven't submitted the preprint yet. Missing periods (all in SI): * At the end of the 'Adding Data" brimx section * On the next page at the end of the "Likewise........csv file" paragraph * Top of page 11 * End of second paragraph on page 11 * developper --> developer in the same sentence as above Sorry on my phone otherwise I'd try to explain more clearly, but other than those it looks great and ready to submit! Well done everyone, Cheers, Sal Sent from Outlook for Android<https://aka.ms/AAb9ysg> ________________________________ From: Kareem Elsayad via Software <software@biobrillouin.org> Sent: Friday, September 5, 2025 11:15:43 AM To: Software Mailing list <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> Reply to: Robert Prevedel <prevedel@embl.de> Date: Friday, 5. September 2025 at 09:11 To: Software Mailing list <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 http://www.prevedel.embl.de This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

Great, thanks Robert! From: Robert Prevedel via Software <software@biobrillouin.org> Reply to: Robert Prevedel <prevedel@embl.de> Date: Sunday, 7. September 2025 at 11:30 To: "Sal La Cavera III (staff)" <Salvatore.LaCaveraIII@nottingham.ac.uk> Cc: Software Mailing list <software@biobrillouin.org> Subject: [Software] Re: Paper preprint Dear all, thanks for the last minute input - I’ve included it all and submitted! Below is the email - let’s hope they screen it in time for Pierre’s deadline on Wed. As soon as I get the permanent ID I will forward it. Let’s see whether and what feedback we get through the preprint and newsletter, and let’s aim to submit to Nature Methods in a week or two?! Have a lovely Sunday everyone, 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 Begin forwarded message: From: bioRxiv@openrxiv.org Subject: bioRxiv Manuscript Received Date: 7. September 2025 at 11:25:42 CEST To: prevedel@embl.de, prevedel@embl.de MS ID#: BIORXIV/2025/674600 MS TITLE: A standardized file format and open-source analysis framework for Brillouin microscopy data Dear Robert Prevedel; This is an automatic message acknowledging your online submission to bioRxiv. Completion of article screening typically takes around 24-72 hours; however, it may take longer over a weekend or holiday. If you would like to make changes to your submission prior to it being approved for posting on bioRxiv, log in to your author area, click on the "Manuscripts Undergoing Screening" section and select "Request Return of Manuscript" for the corresponding MS ID you would like us to return. Do not create a new submission to update your manuscript as this will create a duplicate submission and will significantly delay the screening of your manuscript. In addition, note that bioRxiv now allows you to save time submitting to certain journals or review services by transmitting your manuscript files and metadata directly.To submit your paper to a journal, please click on the link below to access your "Submit bioRxiv Preprint to a Journal or Peer Review" queue: (https://submit.biorxiv.org/submission/queue?queueName=send_paper_away_author) Thank you for your submission. Best wishes, The bioRxiv team On 07.09.2025, at 11:17, Sal La Cavera III (staff) via Software <software@biobrillouin.org> wrote: Hi Robert, Only a couple very minor punctuation edits if you haven't submitted the preprint yet. Missing periods (all in SI): At the end of the 'Adding Data" brimx section On the next page at the end of the "Likewise........csv file" paragraph Top of page 11 End of second paragraph on page 11 developper --> developer in the same sentence as above Sorry on my phone otherwise I'd try to explain more clearly, but other than those it looks great and ready to submit! Well done everyone, Cheers, Sal Sent from Outlook for Android From: Kareem Elsayad via Software <software@biobrillouin.org> Sent: Friday, September 5, 2025 11:15:43 AM To: Software Mailing list <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> Reply to: Robert Prevedel <prevedel@embl.de> Date: Friday, 5. September 2025 at 09:11 To: Software Mailing list <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 http://www.prevedel.embl.de This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law. _______________________________________________ Software mailing list -- software@biobrillouin.org To unsubscribe send an email to software-leave@biobrillouin.org