Proposition of paragraph for next Newsletter
Hi everyone, Following this afternoon’s meeting, here is a proposition for a paragraph for the next newsletter:  The “contact us” sends to a new email sent to “software@biobrillouin.org <mailto:software@biobrillouin.org>” (the address I’m sending this email to), the links to GitHub send to the two GitHub repositories. This is a “by default” version, but if you’d want to change or add things, just tell me, I’m planning on sending the newsletter on Monday. Best, Pierre PS: sorry if I was grumpy during the meeting, I’ve been trying to convince a spectrometer to work for weeks and I am starting to think it has a will of its own and that its will is entirely focused on making sure it does NOT work… I guess that’s what makes research “fun” Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria
Thanks Pierre! Sounds good in general, but I suggest small changes: Title: Beta testers for file formats… We are looking for beta testers to help us develop ways to store... I.e. leave out the ‘unifying’ parts so it’s not confusing (which is also something we need to make sure in the paper). 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
On 28.08.2025, at 17:33, Pierre Bouvet via Software <software@biobrillouin.org> wrote:
Hi everyone,
Following this afternoon’s meeting, here is a proposition for a paragraph for the next newsletter: <Screenshot 2025-08-28 at 17.25.20.png>
The “contact us” sends to a new email sent to “software@biobrillouin.org <mailto:software@biobrillouin.org>” (the address I’m sending this email to), the links to GitHub send to the two GitHub repositories. This is a “by default” version, but if you’d want to change or add things, just tell me, I’m planning on sending the newsletter on Monday.
Best,
Pierre
PS: sorry if I was grumpy during the meeting, I’ve been trying to convince a spectrometer to work for weeks and I am starting to think it has a will of its own and that its will is entirely focused on making sure it does NOT work… I guess that’s what makes research “fun”
Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria
_______________________________________________ Software mailing list -- software@biobrillouin.org To unsubscribe send an email to software-leave@biobrillouin.org
Changed :) Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria
On 28/8/25, at 17:41, Robert Prevedel <prevedel@embl.de> wrote:
Thanks Pierre!
Sounds good in general, but I suggest small changes:
Title: Beta testers for file formats…
We are looking for beta testers to help us develop ways to store...
I.e. leave out the ‘unifying’ parts so it’s not confusing (which is also something we need to make sure in the paper).
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
On 28.08.2025, at 17:33, Pierre Bouvet via Software <software@biobrillouin.org> wrote:
Hi everyone,
Following this afternoon’s meeting, here is a proposition for a paragraph for the next newsletter: <Screenshot 2025-08-28 at 17.25.20.png>
The “contact us” sends to a new email sent to “software@biobrillouin.org <mailto:software@biobrillouin.org>” (the address I’m sending this email to), the links to GitHub send to the two GitHub repositories. This is a “by default” version, but if you’d want to change or add things, just tell me, I’m planning on sending the newsletter on Monday.
Best,
Pierre
PS: sorry if I was grumpy during the meeting, I’ve been trying to convince a spectrometer to work for weeks and I am starting to think it has a will of its own and that its will is entirely focused on making sure it does NOT work… I guess that’s what makes research “fun”
Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria
_______________________________________________ Software mailing list -- software@biobrillouin.org To unsubscribe send an email to software-leave@biobrillouin.org
Hi Pierre, thanks for preparing a draft. I would also add a point about the brimview webapp, something like: * BrimView: a webapp to explore both local and cloud based brim files (https://biobrillouin.org/brimview/ (https://biobrillouin.org/brimview/)) We would first need to fix some bugs though, and this will most likely not be done by monday... could you wait a couple of days? Best, Carlo On Thu, Aug 28, 2025 at 17:34, Pierre Bouvet via Software wrote: Hi everyone, Following this afternoon’s meeting, here is a proposition for a paragraph for the next newsletter: The “contact us” sends to a new email sent to “software@biobrillouin.org (mailto:software@biobrillouin.org)” (the address I’m sending this email to), the links to GitHub send to the two GitHub repositories. This is a “by default” version, but if you’d want to change or add things, just tell me, I’m planning on sending the newsletter on Monday. Best, Pierre PS: sorry if I was grumpy during the meeting, I’ve been trying to convince a spectrometer to work for weeks and I am starting to think it has a will of its own and that its will is entirely focused on making sure it does NOT work… I guess that’s what makes research “fun” Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria
Hi everyone, Following a mail I sent Carlo this morning, here is a first version of a document I made to help first timers use the HDF5_BLS library. The idea is to send this PDF together with a demo Python script to people answering the newsletter call so they can follow a rapid tutorial on how to use the library and rapidly give us their feedback. I’ll make a second document on how to use the treatment soon. The sources are at https://github.com/bio-brillouin/HDF5_BLS/tree/main/guides/Library_Test Best, Pierre Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria 
On 28/8/25, at 22:42, Carlo Bevilacqua via Software <software@biobrillouin.org> wrote:
Hi Pierre, thanks for preparing a draft.
I would also add a point about the brimview webapp, something like: BrimView: a webapp to explore both local and cloud based brim files (https://biobrillouin.org/brimview/) We would first need to fix some bugs though, and this will most likely not be done by monday... could you wait a couple of days?
Best, Carlo
On Thu, Aug 28, 2025 at 17:34, Pierre Bouvet via Software <software@biobrillouin.org> wrote: Hi everyone,
Following this afternoon’s meeting, here is a proposition for a paragraph for the next newsletter: <Screenshot 2025-08-28 at 17.25.20.png>
The “contact us” sends to a new email sent to “software@biobrillouin.org <mailto:software@biobrillouin.org>” (the address I’m sending this email to), the links to GitHub send to the two GitHub repositories. This is a “by default” version, but if you’d want to change or add things, just tell me, I’m planning on sending the newsletter on Monday.
Best,
Pierre
PS: sorry if I was grumpy during the meeting, I’ve been trying to convince a spectrometer to work for weeks and I am starting to think it has a will of its own and that its will is entirely focused on making sure it does NOT work… I guess that’s what makes research “fun”
Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria
_______________________________________________ Software mailing list -- software@biobrillouin.org To unsubscribe send an email to software-leave@biobrillouin.org
Very nice! One idea might be to also create a kind of online questionnaire they fill in before getting software and one after regarding their experience (what part they found most useful, what is its biggest strength, what they use it for, but also negatives). In the event that we can convince enough people to do, then can even include lines in manuscript alluding to this beta testing like (from questionnaire before): X out of X beta testers used X-type of spectrometers combined with a confocal microscope and had a background in Biology”.. (and from after) …out of X people that used X, X of them identified X as the most useful feature or Y used this feature. Long term this can allow us to also track demographic of people who download (main user base) if they have to somehow fill in prior to downloading (but I guess that’s tricky to program and not feasible if free on github etc., so would have to be a voluntary thing) From: Pierre Bouvet via Software <software@biobrillouin.org> Reply to: Pierre Bouvet <pierre.bouvet@meduniwien.ac.at> Date: Friday, 29. August 2025 at 13:36 To: Software Mailing list <software@biobrillouin.org> Subject: [Software] Re: [EXTERN] Re: Proposition of paragraph for next Newsletter Hi everyone, Following a mail I sent Carlo this morning, here is a first version of a document I made to help first timers use the HDF5_BLS library. The idea is to send this PDF together with a demo Python script to people answering the newsletter call so they can follow a rapid tutorial on how to use the library and rapidly give us their feedback. I’ll make a second document on how to use the treatment soon. The sources are at https://github.com/bio-brillouin/HDF5_BLS/tree/main/guides/Library_Test Best, Pierre Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria
Hi Pierre and all, great to see the documentation coming together - I think that’s highly useful! Just a couple quick thoughts: I think it would be strategically wise to make a coherent and as concise (tutorial) document that encompasses all aspects of our work, i.e. also including the Brim, BrimView and BrimConverter parts. Otherwise there’s a big chance that the general user gets confused and overloaded by several different support documents. I think for the newsletter it’d be fine to just point to the Github pages as you drafted originally. For the newsletter announcement: I just spoke to Carlo and he’s confident he’ll iron out the last kinks early next week, so please wait just a couple days more until you get our o.k. for this. Alternatively, if the newsletter can’t wait, we could send a separate email to the BioBrillouin list about this once all parts are in place (code, documentation, etc.). Have a nice weekend 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
On 29.08.2025, at 16:13, Kareem Elsayad via Software <software@biobrillouin.org> wrote:
Very nice!
One idea might be to also create a kind of online questionnaire they fill in before getting software and one after regarding their experience (what part they found most useful, what is its biggest strength, what they use it for, but also negatives). In the event that we can convince enough people to do, then can even include lines in manuscript alluding to this beta testing like (from questionnaire before): X out of X beta testers used X-type of spectrometers combined with a confocal microscope and had a background in Biology”.. (and from after) …out of X people that used X, X of them identified X as the most useful feature or Y used this feature. Long term this can allow us to also track demographic of people who download (main user base) if they have to somehow fill in prior to downloading (but I guess that’s tricky to program and not feasible if free on github etc., so would have to be a voluntary thing)
From: Pierre Bouvet via Software <software@biobrillouin.org <mailto:software@biobrillouin.org>> Reply to: Pierre Bouvet <pierre.bouvet@meduniwien.ac.at <mailto:pierre.bouvet@meduniwien.ac.at>> Date: Friday, 29. August 2025 at 13:36 To: Software Mailing list <software@biobrillouin.org> Subject: [Software] Re: [EXTERN] Re: Proposition of paragraph for next Newsletter
Hi everyone,
Following a mail I sent Carlo this morning, here is a first version of a document I made to help first timers use the HDF5_BLS library. The idea is to send this PDF together with a demo Python script to people answering the newsletter call so they can follow a rapid tutorial on how to use the library and rapidly give us their feedback. I’ll make a second document on how to use the treatment soon. The sources are at https://github.com/bio-brillouin/HDF5_BLS/tree/main/guides/Library_Test
Best,
Pierre
Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria
_______________________________________________ Software mailing list -- software@biobrillouin.org To unsubscribe send an email to software-leave@biobrillouin.org
Hi Robert, I fully agree, I suggest adding the steps for using the format you have developed directly to the LaTex document, based on the already provided code for creating synthetic data (the source for the LaTex document is located at: https://github.com/bio-brillouin/HDF5_BLS/tree/main/guides/Library_Test). The way I thought about the newsletter is, as you propose, to put the minimal amount of information to catch people’s interest, and then send them a unified PDF (testing HDF5+testing Zarr+how to use the treatment package) with essentially a tutorial that first presents a replicable example and then opens to an integration in existing codes to get an initial feedback. For the newsletter, I can technically wait as long as I want but because the deadline for abstract submission to BioBrillouin falls on October 1st, I think it would be best not too wait too long either (although most people might not need the reminder). I was therefore thinking of sending the newsletter by the end of the week. Since we’ll then send people the PDF, this would buy at least 1 and potentially 2 weeks for fixing the bugs you have found in your code and writing your steps to test your solutions. Following Kareem’s idea, I’ve put together a list of questions (cf. document attached) we could build on to ask people for feedback. Don’t hesitate to modify it! Best, Pierre Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria 
On 29/8/25, at 21:00, Robert Prevedel via Software <software@biobrillouin.org> wrote:
Hi Pierre and all,
great to see the documentation coming together - I think that’s highly useful! Just a couple quick thoughts: I think it would be strategically wise to make a coherent and as concise (tutorial) document that encompasses all aspects of our work, i.e. also including the Brim, BrimView and BrimConverter parts. Otherwise there’s a big chance that the general user gets confused and overloaded by several different support documents. I think for the newsletter it’d be fine to just point to the Github pages as you drafted originally.
For the newsletter announcement: I just spoke to Carlo and he’s confident he’ll iron out the last kinks early next week, so please wait just a couple days more until you get our o.k. for this. Alternatively, if the newsletter can’t wait, we could send a separate email to the BioBrillouin list about this once all parts are in place (code, documentation, etc.).
Have a nice weekend 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
On 29.08.2025, at 16:13, Kareem Elsayad via Software <software@biobrillouin.org> wrote:
Very nice!
One idea might be to also create a kind of online questionnaire they fill in before getting software and one after regarding their experience (what part they found most useful, what is its biggest strength, what they use it for, but also negatives). In the event that we can convince enough people to do, then can even include lines in manuscript alluding to this beta testing like (from questionnaire before): X out of X beta testers used X-type of spectrometers combined with a confocal microscope and had a background in Biology”.. (and from after) …out of X people that used X, X of them identified X as the most useful feature or Y used this feature. Long term this can allow us to also track demographic of people who download (main user base) if they have to somehow fill in prior to downloading (but I guess that’s tricky to program and not feasible if free on github etc., so would have to be a voluntary thing)
From: Pierre Bouvet via Software <software@biobrillouin.org <mailto:software@biobrillouin.org>> Reply to: Pierre Bouvet <pierre.bouvet@meduniwien.ac.at <mailto:pierre.bouvet@meduniwien.ac.at>> Date: Friday, 29. August 2025 at 13:36 To: Software Mailing list <software@biobrillouin.org> Subject: [Software] Re: [EXTERN] Re: Proposition of paragraph for next Newsletter
Hi everyone,
Following a mail I sent Carlo this morning, here is a first version of a document I made to help first timers use the HDF5_BLS library. The idea is to send this PDF together with a demo Python script to people answering the newsletter call so they can follow a rapid tutorial on how to use the library and rapidly give us their feedback. I’ll make a second document on how to use the treatment soon. The sources are at https://github.com/bio-brillouin/HDF5_BLS/tree/main/guides/Library_Test
Best,
Pierre
Pierre Bouvet, PhD Post-doctoral Fellow Medical University Vienna Department of Anatomy and Cell Biology Wahringer Straße 13, 1090 Wien, Austria
_______________________________________________ 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
participants (4)
-
Carlo Bevilacqua -
Kareem Elsayad -
Pierre Bouvet -
Robert Prevedel