From a8ce6d4690feb86d6224431e1b4ee0ad0170c908 Mon Sep 17 00:00:00 2001 From: cdpaiva Date: Tue, 4 Nov 2025 16:49:51 -0500 Subject: [PATCH 1/3] docs: minor text updates --- paper/paper.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index 0644245..695ebe8 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -35,7 +35,7 @@ bibliography: paper.bib Genetically encoded fluorescent indicators are powerful tools for monitoring biological processes in live samples [@lin:2016; @nakai:2001]. When combined with a large field of view, a single time-lapse recording has the potential to capture many specimens, facilitating high-throughput data collection. -However, the simultaneous recording of many biological samples across time points produces large, multidimensional datasets that are challenging to process and analyze. +However, this approach generates large, multidimensional datasets that are challenging to process and analyze. We present `SNAzzy`, a Python package for studying synchronous network activity (SNA) in Drosophila embryos via high-throughput microscopy. SNA is a hallmark of developing nervous systems [@wu:2024; @blankenship:2009; @akin:2020], often studied using genetically encoded calcium indicators to monitor neural activity in vivo. `SNAzzy` processes and analyzes time-lapse datasets taken from live samples using fluorescent widefield microscopy. @@ -45,9 +45,9 @@ This tool can be readily applied to analyze fluorescent intensities in time-laps # Statement of need -During synchronous network activity (SNA), many neurons fire synchronously, generating waves of activity that span across large portions of the nervous system [@blankenship:2009; @wu:2024; @akin:2020]. +During synchronous network activity (SNA), many neurons fire simultaneously, generating waves of activity that span across large portions of the nervous system [@blankenship:2009; @wu:2024; @akin:2020]. In Drosophila embryos, SNA typically lasts 4 hours, during which the nervous system undergoes a stereotyped morphological change via ventral nerve cord condensation [@crisp:2008; @carreira:2021]. -To gain an understanding of SNA, it is essential to quantify waves of activity in the nervous system while also tracking morphology as a proxy of neurodevelopment. +To gain an understanding of SNA, it is essential to quantify waves of activity in the nervous system while also tracking morphology as a proxy for neurodevelopment. For these reasons, we combine a commonly used genetically encoded calcium indicator (GECI) that reports neural activity with a structural fluorophore [@carreira:2021]. The structural fluorophore signal remains stable, independent of neural activity, making it suitable for continuous tracking morphology of the nerve cord. To record many embryos during SNA, we use a wide-field fluorescence microscopy system that captures the GECI and structural fluorophore signal of dozens of developing embryos for over 5 hours. @@ -140,6 +140,8 @@ A ∆F/F trace (white) and the corresponding peaks (magenta dots) are shown. The low-passed signal (green line) is used as a reference to determine peaks. The GUI enables the modification of analysis parameters, visualization of data, and comparison of metrics across groups of experiments, as well as manual adjustment of peak data.\label{fig:fig4}](figures/snazzy-fig4.png) +# Conclusion + In conclusion, genetically encoded fluorescent indicators and microscopy systems are evolving rapidly, increasing the data acquisition throughput. Custom open-source tools are needed to handle such large data files. `SNAzzy` addresses this by offering an automated, scalable, and user-friendly platform for analyzing synchronous network activity in developing embryos. From e4999f8a53449433b102611ba45f3f8ff7f98229 Mon Sep 17 00:00:00 2001 From: cdpaiva Date: Wed, 5 Nov 2025 11:37:06 -0500 Subject: [PATCH 2/3] docs: add new bib reference --- paper/paper.bib | 14 ++++++++++++++ paper/paper.md | 6 +++--- 2 files changed, 17 insertions(+), 3 deletions(-) diff --git a/paper/paper.bib b/paper/paper.bib index 944577b..303f82f 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -124,6 +124,20 @@ @article{giovannucci:2019 keywords={calcium imaging; data analysis; mouse; neuroscience; one-photon; open source; software; two-photon; zebrafish}, language={en} } +@article{karkali:2022, + title={Condensation of the Drosophila nerve cord is oscillatory and depends on coordinated mechanical interactions}, + volume={57}, + ISSN={1534-5807}, + DOI={10.1016/j.devcel.2022.03.007}, + number={7}, + journal={Developmental cell}, + publisher={Elsevier BV}, + author={Karkali, Katerina and Tiwari, Prabhat and Singh, Anand and Tlili, Sham and Jorba, Ignasi and Navajas, Daniel and Muñoz, José J. and Saunders, Timothy E. and Martin-Blanco, Enrique}, + year={2022}, + month=apr, + pages={867–882.e5}, + language={en} } + @article{lin:2016, title={Genetically encoded indicators of neuronal activity}, volume={19}, diff --git a/paper/paper.md b/paper/paper.md index 695ebe8..52b3cca 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -9,7 +9,7 @@ tags: - Neurodevelopment - Circuit Wiring authors: - - name: Carlos Damiani Paiva + - name: Carlos D. Paiva orcid: 0009-0007-6658-2620 affiliation: "1, 2" - name: Alana J. Evora @@ -27,7 +27,7 @@ affiliations: index: 1 - name: Department of Neurobiology, Duke University, Durham, NC 27708 index: 2 -date: 8 October 2025 +date: 5 November 2025 bibliography: paper.bib --- @@ -46,7 +46,7 @@ This tool can be readily applied to analyze fluorescent intensities in time-laps # Statement of need During synchronous network activity (SNA), many neurons fire simultaneously, generating waves of activity that span across large portions of the nervous system [@blankenship:2009; @wu:2024; @akin:2020]. -In Drosophila embryos, SNA typically lasts 4 hours, during which the nervous system undergoes a stereotyped morphological change via ventral nerve cord condensation [@crisp:2008; @carreira:2021]. +In Drosophila embryos, SNA typically lasts 4 hours, during which the nervous system undergoes a stereotyped morphological change via ventral nerve cord condensation [@crisp:2008; @carreira:2021; @karkali:2022]. To gain an understanding of SNA, it is essential to quantify waves of activity in the nervous system while also tracking morphology as a proxy for neurodevelopment. For these reasons, we combine a commonly used genetically encoded calcium indicator (GECI) that reports neural activity with a structural fluorophore [@carreira:2021]. The structural fluorophore signal remains stable, independent of neural activity, making it suitable for continuous tracking morphology of the nerve cord. From b4326c2fc61690e5f0dbeaf7dd55ff0496a87481 Mon Sep 17 00:00:00 2001 From: cdpaiva Date: Thu, 6 Nov 2025 13:23:06 -0500 Subject: [PATCH 3/3] docs: update date field --- paper/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paper/paper.md b/paper/paper.md index 52b3cca..a0ad3a4 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -27,7 +27,7 @@ affiliations: index: 1 - name: Department of Neurobiology, Duke University, Durham, NC 27708 index: 2 -date: 5 November 2025 +date: 6 November 2025 bibliography: paper.bib ---