Text review

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}, 

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
@@ -27,15 +27,15 @@ affiliations:
     index: 1
   - name: Department of Neurobiology, Duke University, Durham, NC 27708
     index: 2
-date: 8 October 2025
+date: 6 November 2025
 bibliography: paper.bib
 ---
 
 # Summary
 
 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].
-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.
+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; @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.
 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.