Calcium imaging analysis — lab heads

Consent

Consent * I consent to my responses being used for this research.

Quotation preference * Happy to be quoted by name Happy to be quoted anonymously (e.g. “a PI at a UK institute”) Please do not quote me

Section 1 — Your lab

A1. Institution and country (optional)

A2. Your role * Group leader / PI Co-investigator / senior research fellow Lab manager with budget responsibility Other

A3. How many people work in your lab? * 1–3 4–7 8–15 16+

A4. Does your lab generate calcium imaging data? * key Yes, routinely (it is a core method for us) Yes, occasionally No — we reuse public or collaborators' data No

A5. Which imaging do you do? (select all) Two-photon, in vivo One-photon miniscope, freely moving Widefield / mesoscale Confocal or slice imaging Light-sheet Organoid / iPSC-derived cultures Other

A6. Which tools does your lab use to process calcium imaging data? (select all) * key Suite2p CaImAn Inscopix IDPS EZcalcium Custom MATLAB scripts Custom Python scripts Imaris / Aivia / arivis We outsource it Other

A7. Roughly how many imaging datasets does your lab analyse per year? Fewer than 10 10–50 50–200 More than 200

A8. Do you deposit data in DANDI or a similar archive? Yes, routinely Sometimes No Not yet, but a funder will require it soon

Section 2 — What actually happens

Please answer from memory of real events, not the ideal case.

A9. Think about the MOST RECENT calcium imaging dataset your lab took from acquisition to a figure you would show in lab meeting. Roughly how long did that take, in working days? * key working days

A10. Roughly what share of that time went to each stage?

Item	0–10%	11–25%	26–50%	51–75%	76–100%
Preprocessing (motion correction, segmentation)	Preprocessing (motion correction, segmentation) — 0–10%	Preprocessing (motion correction, segmentation) — 11–25%	Preprocessing (motion correction, segmentation) — 26–50%	Preprocessing (motion correction, segmentation) — 51–75%	Preprocessing (motion correction, segmentation) — 76–100%
Curation and quality control	Curation and quality control — 0–10%	Curation and quality control — 11–25%	Curation and quality control — 26–50%	Curation and quality control — 51–75%	Curation and quality control — 76–100%
Downstream analysis	Downstream analysis — 0–10%	Downstream analysis — 11–25%	Downstream analysis — 26–50%	Downstream analysis — 51–75%	Downstream analysis — 76–100%
Interpretation and writing up	Interpretation and writing up — 0–10%	Interpretation and writing up — 11–25%	Interpretation and writing up — 26–50%	Interpretation and writing up — 51–75%	Interpretation and writing up — 76–100%

0–10%

11–25%

26–50%

51–75%

76–100%

Preprocessing (motion correction, segmentation)

Curation and quality control

Downstream analysis

Interpretation and writing up

A11. In the last 12 months, has your lab had to REDO an analysis because a problem was found late? * key Yes, more than once Yes, once No Don't know

A12. If yes — what went wrong? (optional)

A13. Select your TOP 3 bottlenecks * key

Select at most 3.

Preprocessing takes too long ROI / cell segmentation quality is unreliable Different lab members analyse the same data differently Hard to know whether a result is trustworthy Interpreting and writing up takes too long Reproducing an analysis done months ago Training new lab members to do the analysis Connecting our results to the wider literature Other

Section 3 — The concept

Please read this before answering. It is written plainly and without sales language, on purpose.

A system that takes calcium imaging data you have ALREADY PREPROCESSED (for example Suite2p or CaImAn output, or an NWB file), and then works through the analysis the way a careful lab member would: checking the data is what you think it is, assessing whether quality supports a conclusion, inferring spikes, characterising population activity, producing figures, and writing a report.

It shows you every line of code it ran. It pauses and asks for your approval before moving to the next stage. It records what it did so the analysis can be re-run exactly later.

It does NOT currently do motion correction or cell segmentation. It picks up after those.

A14. How valuable would each of these be to your lab? *

Item	Not valuable	Somewhat valuable	Very valuable	Would change how we work
Runs the analysis and shows the code it ran	Runs the analysis and shows the code it ran — Not valuable	Runs the analysis and shows the code it ran — Somewhat valuable	Runs the analysis and shows the code it ran — Very valuable	Runs the analysis and shows the code it ran — Would change how we work
Flags when data quality is too poor to support a conclusion	Flags when data quality is too poor to support a conclusion — Not valuable	Flags when data quality is too poor to support a conclusion — Somewhat valuable	Flags when data quality is too poor to support a conclusion — Very valuable	Flags when data quality is too poor to support a conclusion — Would change how we work
Refuses to analyse a file that isn't what you assumed it was	Refuses to analyse a file that isn't what you assumed it was — Not valuable	Refuses to analyse a file that isn't what you assumed it was — Somewhat valuable	Refuses to analyse a file that isn't what you assumed it was — Very valuable	Refuses to analyse a file that isn't what you assumed it was — Would change how we work
Produces a written report with figures	Produces a written report with figures — Not valuable	Produces a written report with figures — Somewhat valuable	Produces a written report with figures — Very valuable	Produces a written report with figures — Would change how we work
Reproduces an analysis exactly, months later	Reproduces an analysis exactly, months later — Not valuable	Reproduces an analysis exactly, months later — Somewhat valuable	Reproduces an analysis exactly, months later — Very valuable	Reproduces an analysis exactly, months later — Would change how we work
Standardises analysis across everyone in the lab	Standardises analysis across everyone in the lab — Not valuable	Standardises analysis across everyone in the lab — Somewhat valuable	Standardises analysis across everyone in the lab — Very valuable	Standardises analysis across everyone in the lab — Would change how we work
Suggests sensible next analyses	Suggests sensible next analyses — Not valuable	Suggests sensible next analyses — Somewhat valuable	Suggests sensible next analyses — Very valuable	Suggests sensible next analyses — Would change how we work
Links findings to relevant published papers	Links findings to relevant published papers — Not valuable	Links findings to relevant published papers — Somewhat valuable	Links findings to relevant published papers — Very valuable	Links findings to relevant published papers — Would change how we work

Not valuable

Somewhat valuable

Very valuable

Would change how we work

Runs the analysis and shows the code it ran

Flags when data quality is too poor to support a conclusion

Refuses to analyse a file that isn't what you assumed it was

Produces a written report with figures

Reproduces an analysis exactly, months later

Standardises analysis across everyone in the lab

Suggests sensible next analyses

Links findings to relevant published papers

A15. What would you need before you would let a system like this produce a figure that goes into one of your papers? (select all) * key Being able to read the code it ran Benchmarking it against an analysis my lab did manually Published, peer-reviewed validation A human approval step at every stage A colleague I trust having used it successfully Being able to run it on data where I already know the answer Nothing would convince me — I would not use an automated system for this Other

A16. Suppose a FREE, open-source version of this existed. What, if anything, would make you pay for a supported commercial version instead? (select all) * key Support when it breaks Guaranteed reproducibility and long-term availability Someone accountable if the result is wrong It having passed our institution's IT / security review Time saved that I would otherwise pay a postdoc for Training for lab members Nothing — I would use the free one Other

Section 4 — Budget and authority

A17. Does your lab currently pay for any data analysis software? * Yes No Don't know — the facility or department handles it

A17b. If yes — which, and roughly how much per year?

A18. If you wanted software like this, which budget would it come from? * key Grant — consumables / directly incurred Grant — equipment Core facility recharge Departmental or institutional budget Discretionary / unrestricted funds No budget line exists for this Don't know

A19. Who signs off a £3,000/year software purchase for your lab? * key Me, alone Me, with departmental approval Facility or department decides Central procurement Don't know

A20a. Thinking about a supported annual subscription for your lab, covering analysis of your own data, with support and training — at what annual price would it be SO LOW you would question its quality? * key

Please give your own honest figures. There is no right answer, and we have deliberately not suggested one.

£ per year

A20b. At what annual price would it be a BARGAIN — clearly good value? * key £ per year

A20c. At what annual price would it start to feel EXPENSIVE, but still worth considering? * key £ per year

A20d. At what annual price would it be SO EXPENSIVE you would not consider it? * key £ per year

A21. If your institution has an imaging core facility, would it be more natural for THE FACILITY to buy this centrally than for your lab to buy it? Yes, much more natural Possibly No, we would buy our own We have no such facility

Section 5 — Commitment

This section matters more to us than any other. Please only tick what you would genuinely do.

A22. Which of the following would you be willing to do? (select all) * key Try it once on a PUBLIC dataset Try it on ONE OF YOUR OWN datasets Let a lab member spend 2 hours being onboarded Provide a dataset AND your lab's own analysis of it, so we can benchmark against you Be named publicly as a design partner Sign a non-binding letter of intent to purchase at a stated price Pay a deposit for early access None of the above

A23. Would you be willing to introduce us to anyone else who should see this? Yes — another academic lab Yes — a core facility Yes — an industry contact No

A24. Is there anything we have not asked about that we should have?