Hi all,

Following our meeting, I've made the changes to my proposed schema/logo: 

- "Unified Brillouin Scattering Toolkit" for the title
- Brimfile: BLS Bio-image application
- HDF5_BLS: Biophysics & data processing

Are we all fine with the text ? 

Here's also the svg : https://drive.google.com/drive/folders/1gbkEb_Sdsf86yCNoDhwoNXqoU2iJgXcu?usp=sharing  and I'll put my poster there too later

Best, 

Sebastian Hambura
Software Engineer
Robert Prevedel Group 
Cell Biology and Biophysics 
EMBL Heidelberg
Meyerhofstraße 1
69117 Heidelberg, Germany
Am 06.11.2025 um 14:44 schrieb Pierre Bouvet via Software:
Hi Sebastian,

I really like your idea and visual! I don’t think on our side at least the colors will be a problem so as long as you have thumbs up on your side we should be OK. 
The only two remarks I have are
1 -  The HDF5_BLS project is not only a unified solution for data processing in BLS but also for storing data from all BLS modalities (and any other complimentary modality).
2 - BrimView is not compatible with the HDF5_BLS project, and from what I understand, only uses the HDF5_BLS_treat package for the integrated algorithm you have defined (ie: it does not take advantage of the modularity of algorithms at the core of the module, it does not allow the user to go through the algorithm to change any of the parameters of the functions - eg the size of the window before the fit or the boundary conditions on the linewidth, is not able to run a stored HDF5_BLS_treat algorithm and does not allow neither import nor export of these algorithms as standalone JSON files).
This is why I thought going with a “non-BLS end-users” vs “BLS researchers” was more interesting: it allowed to logically differentiate our two approaches without opposing them as the needs of these two communities are very different (the analogy I made with high-level and low-level programming). 

Let me know what you think :)

Pierre

Pierre Bouvet, PhD
Post-doctoral Fellow
Medical University Vienna
Department of Anatomy and Cell Biology
Wahringer Straße 13, 1090 Wien, Austria





On 6/11/25, at 14:11, Sebastian Hambura via Software <software@biobrillouin.org> wrote:

Hi Pierre, 


I like your idea of having some reference to the other presentations. Maybe instead of a dichotomy, we could reference all 3 presentations ? See attached my attempt. 

On my poster BrimView would be on top and "highlighted" in green, on your poster the HDF5_BLS one, and on Carlo's the BrimFile. (The color palette should work with EMBL green and meduniwien green - the one from the webpage). 


<KSrWrdrRpXoqZQuC.png>

(FYI: I made the SVG with inkscape, and for me it doesn't display as expected with Edge)


Best, 

Sebastian

Sebastian Hambura
Software Engineer
Robert Prevedel Group 
Cell Biology and Biophysics 
EMBL Heidelberg
Meyerhofstraße 1
69117 Heidelberg, Germany
Am 05.11.2025 um 09:59 schrieb Pierre Bouvet via Software:
Hi @ll :)

Great news for the preprint, thanks Robert! :) 
Following the idea of presenting the projects as complimenting each other on the presentation supports, I propose to assign a project for a use case and more globally a user. 
For Brim, you are focusing on spatial maps for non-BLS experts, for HDF5_BLS I focus on unifying treatments and analysis independently of BLS modality, targeting therefore BLS researchers. Visually we could therefore divide the users in “BLS experts” and “BLS end-users”. Orally we could use the analogy with high-level programming for Brim (low user complexity, low adaptability) and low-level programming for HDF5_BLS (higher user complexity, higher adaptability), and underline the use of the same treatment algorithms and the ability to export from HDF5_BLS to Brim spatial images. 
Here is a svg file with a schematic to illustrate this idea simply. If this is OK with you, we could add this to the poster and oral presentation supports.

Best,

Pierre

Pierre Bouvet, PhD
Post-doctoral Fellow
Medical University Vienna
Department of Anatomy and Cell Biology
Wahringer Straße 13, 1090 Wien, Austria





On 4/11/25, at 15:53, Sal La Cavera III (staff) via Software <software@biobrillouin.org> wrote:

That is awesome news, well chased Robert! :)

---------------------------------------------------------------
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
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Book a Coffee and Research chat with me!
From: Robert Prevedel <prevedel@embl.de>
Sent: 03 November 2025 20:58
To: Sal La Cavera III (staff) <Salvatore.LaCaveraIII@nottingham.ac.uk>
Cc: Kareem Elsayad via Software <software@biobrillouin.org>
Subject: Re: [Software] Meeting to discuss presentations of software at BioBrillouin 2025
 
Dear all,
great news - seems like the reminder helped ;-)
Cheers,
Robert



Begin forwarded message:

From: Nina Vogt <nina.vogt@us.nature.com>
Subject: Re: Proposal for a Correspondence on Standardization in Brillouin Microscopy (NMETH-C62839)
Date: 3. November 2025 at 21:34:24 CET
To: Robert Prevedel <prevedel@embl.de>
Cc: Kareem Elsayad <kareem.elsayad@meduniwien.ac.at>

Dear Robert,

Thanks for getting in touch. I am sorry about the further delays. But I have managed to read your manuscript, and we have decided to send your manuscript out for peer review. I simply haven’t had a chance to assign reviewers yet, which is the reason that you haven’t received a notification. I should be able to assign reviewers later today though. Thanks for understanding.

Best,
Nina

From: Robert Prevedel <prevedel@embl.de>
Date: Monday, November 3, 2025 at 3:31 PM
To: Nina Vogt <nina.vogt@us.nature.com>
Cc: Kareem Elsayad <kareem.elsayad@meduniwien.ac.at>
Subject: Re: Proposal for a Correspondence on Standardization in Brillouin Microscopy (NMETH-C62839)

This Message Is From an External Sender
This message came from outside your organization.
 
Dear Nina,

I hope you are doing well. I wanted to kindly follow up on our manuscript entitled “A standardized file format and open-source analysis framework for Brillouin microscopy data,” which we submitted on September 17, 2025 (NMETH-C62839).

We completely understand how demanding the current circumstances must be and truly appreciate your efforts and care that you put into handling submissions.

We remain very enthusiastic about the possibility of publishing this work in Nature Methods. Given the growing interest in Brillouin microscopy and the increasing need for data standardization, we believe our contribution comes at a particularly timely moment for the field.

Whenever convenient, we would be grateful for any brief update you might be able to share regarding the status of our submission or the review process.

With warm regards and many thanks again for your time and effort,

Robert 
(on behalf of all authors)
-- 
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 03.11.2025, at 15:46, Sal La Cavera III (staff) <Salvatore.LaCaveraIII@nottingham.ac.uk> wrote:

Hi Robert,

Ah ok yeah that makes sense, but also like you said that's quite a long time! Hopefully Nina likes it though, fingers crossed.

---------------------------------------------------------------
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
<Outlook-fwnuyhf3.png>
Book a Coffee and Research chat with me!
From: Robert Prevedel <prevedel@embl.de>
Sent: 03 November 2025 12:14
To: Sal La Cavera III (staff) <Salvatore.LaCaveraIII@nottingham.ac.uk>
Cc: Kareem Elsayad via Software <software@biobrillouin.org>
Subject: Re: [Software] Meeting to discuss presentations of software at BioBrillouin 2025
 
Hi Sal,

I emailed the editor one month ago already and got the response they are understaffed and we should be patient. Nevertheless I think by now it’s ok to re-inquire - I’ve never had a paper sit with an editor that long. If they don’t like it they should at least tell us so we’re not loosing more time. I am gonna email her later today or tomorrow, let’s hope for the best!

Cheers,
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
http://www.prevedel.embl.de






On 03.11.2025, at 11:34, Sal La Cavera III (staff) <Salvatore.LaCaveraIII@nottingham.ac.uk> wrote:

Hi everyone,

Yes totally agree re: coordinating a coherent team message for the different presentations. I'm mainly free on those Mon/Tues slots.

On a side note, it still looks like the manuscript hasn't passed the editorial sift. Does anyone have any intel on that or is it worth a friendly email to Nina asking how it's going?

Looking forward to seeing everyone in Berlin,

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
<Outlook-0n0qekvu.png>
Book a Coffee and Research chat with me!
  
From: Robert Prevedel via Software <software@biobrillouin.org>
Sent: 03 November 2025 08:24
To: Kareem Elsayad <kareem.elsayad@meduniwien.ac.at>
Cc: Kareem Elsayad via Software <software@biobrillouin.org>
Subject: [Software] Re: Meeting to discuss presentations of software at BioBrillouin 2025
 
Hi Kareem,

thanks for organizing - I fully agree it’d be great to coordinate and present a coherent story. I could do the Mon. and Tue. slots, and maybe the Thu. one if really needed. Fri. I am busy.

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
http://www.prevedel.embl.de






On 03.11.2025, at 01:02, Kareem Elsayad via Software <software@biobrillouin.org> wrote:

Hi All,
 
So, at the BioBrillouin meeting in Berlin we have 3 presentations on software stuff ( Carlo=talk, Sebastian=poster, Pierre=Poster) – this is great! Think it would be good if we coordinate a little so as to present coherent message and compliment each others stuff (even directing people to other presentations/posters as relevant).
 
Politically seen, since some (potential) reviewers of manuscript will most likely (certainly) be there, presenting coherent argument of how the different parts are needed for the whole, will look very good. I would propose the idea of having a visual graphic, e.g. a tree or some spider diagram (is that a word?), etc., that everyone includes in their presentation, with e.g. a circle around the part that they are presenting. If I was reviewer from an outside perspective this would look like it really is a serious and coherent thought through effort!
 
Would propose a quick (~1/2 hr) meeting sometime after next week (i.e. 10-14th November)
Below are four times that would work for me.. let me know which could work for you?
 
Mon 10th Nov. 11-12am
Tue 11th Nov. 2-3pm
Thur 13th Nov 12-1pm
Fri 14th Nov 9-10am
 
All the best,
Kareem
 
 
 
 
 
 
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