Mesmerize: a dynamically adaptable user-friendly analysis platform for 2D &amp; 3D calcium imaging data

Kolar, Kushal; Dondorp, Daniel; Zwiggelaar, Jordi Cornelis; Hoyer, Jorgen; Chatzigeorgiou, Marios

doi:10.1101/840488

Cited by 5 publications

(5 citation statements)

References 85 publications

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“…Embryos were perfused with control solution for 5 minutes followed by an exchange of the control solution with the drug solution and subsequently we imaged for 15 minutes (3 movies each 5 minutes long). All movies were acquired at 10fps and subsequently analyzed using Mesmerize v0.1 89 for motion correction, signal extraction, downstream analysis and for producing some of the figures.…”

Section: Methodsmentioning

confidence: 99%

Mapping calcium dynamics in a developing tubular structure

Hoyer¹,

Saba²,

Dondorp³

et al. 2020

Preprint

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Calcium is a ubiquitous and versatile second messenger that plays a central role in the development and function of a wide range of cell types, tissues and organs. Despite significant recent progress in the understanding of calcium (Ca2+) signalling in organs such as the developing and adult brain, we have relatively little knowledge of the contribution of Ca2+ to the development of tubes, structures widely present in multicellular organisms. Here we image Ca2+ dynamics in the developing notochord of Ciona intestinalis. We show that notochord cells exhibit distinct Ca2+ dynamics during specific morphogenetic events such as cell intercalation, cell elongation and tubulogenesis. We used an optogenetically controlled Ca2+ actuator to show that sequestration of Ca2+ results in defective notochord cell intercalation, and pharmacological inhibition to reveal that stretch-activated ion channels (SACs), inositol triphosphate receptor (IP3R) signalling, Store Operated Calcium Entry (SOCE), Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) and gap junctions are required for regulating notochord Ca2+ activity during tubulogenesis. Cytoskeletal rearrangements drive the cell shape changes that accompany tubulogenesis. In line with this, we show that Ca2+ signalling modulates reorganization of the cytoskeletal network across the morphogenetic events leading up to and during tubulogenesis of the notochord. We additionally demonstrate that perturbation of the actin cytoskeleton drastically remodels Ca2+ dynamics, suggesting a feedback mechanism between actin dynamics and Ca2+ signalling during notochord development. This work provides a framework to quantitatively define how Ca2+ signalling regulates tubulogenesis using the notochord as model organ, a defining structure of all chordates.

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Section: Methodsmentioning

confidence: 99%

Mapping calcium dynamics in a developing tubular structure

Hoyer¹,

Saba²,

Dondorp³

et al. 2020

Preprint

Self Cite

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“…To capture images of both left and right MN2s using an inverted microscope, Ciona embryos were fixed on a Petri dish on their dorsal side. However, in previous studies most of the embryos were captured from the lateral side, or studies used embedded larvae for live imaging (Okawa et al, 2020;Kolar et al, 2021). Therefore, in this study, we developed a protocol to fix Ciona embryos on their dorsal side (see Materials and Methods).…”

Section: Activities Of Left and Right Mn2s (St22 -St34) Classified In...mentioning

confidence: 99%

Transitions of motor neuron activities during Ciona development

Utsumi

Oka

Hotta

2023

Front. Cell Dev. Biol.

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Motor neurons (MNs) are one of the most important components of Central Pattern Generators (CPG) in vertebrates (Brown, Proceedings of The Royal Society B: Biological Sciences (The Royal Society), 1911, 84(572), 308–319). However, it is unclear how the neural activities of these components develop during their embryogenesis. Our previous study revealed that in Ciona robusta (Ciona intestinalis type A), a model organism with a simple neural circuit, a single pair of MNs (MN2L/MN2R) was determining the rhythm of its spontaneous early motor behavior (developmental stage St.22-24). MN2s are known to be one of the main components of Ciona CPG, though the neural activities of MN2s in the later larval period (St.25-) were not yet investigated. In this study, we investigated the neural activities of MN2s during their later stages and how they are related to Ciona’s swimming CPG. Long-term simultaneous Ca2+ imaging of both MN2s with GCaMP6s/f (St.22-34) revealed that MN2s continued to determine the rhythm of motor behavior even in their later larval stages. Their activities were classified into seven phases (I-VII) depending on the interval and the synchronicity of MN2L and MN2R Ca2+ transients. Initially, each MN2 oscillates sporadically (I). As they develop into swimming larvae, they gradually oscillate at a constant interval (II-III), then start to synchronize (IV) and fully synchronize (V). Intervals become longer (VI) and sporadic again during the tail aggression period (VII). Interestingly, 76% of the embryos started to oscillate from MN2R. In addition, independent photostimulations on left and right MN2s were conducted. This is the first report of the live imaging of neural activities in Ciona’s developing swimming CPG. These findings will help to understand the development of motor neuron circuits in chordate animals.

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“…Among the methods that provide more detailed information about the kinetics of Ca2+ movements in the cell, confocal microscopy is the most commonly used (Price et al, 2014). However, there are only a few open tools available for its analysis (Schneider et al, 2012;JuholaPenttinen et al, 2015;PenPnen et al, 2015;Giovannucci et al, 2019;PsarasMargara et al, 2021;Pascalin et al, 2022), and are usually used for general image analysis or the study of specific phenomena or even for the analysis of calcium handling in different types of cells (Kolar et al, 2021;Pachitariu et al, 1507).…”

Section: Introductionmentioning

confidence: 99%

CardIAP: calcium transients confocal image analysis tool

et al. 2023

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One of the main topics of cardiovascular research is the study of calcium (Ca2+) handling, as even small changes in Ca2+ concentration can alter cell functionality (Bers, Annu Rev Physiol, 2014, 76, 107–127). Ionic calcium (Ca2+) plays the role of a second messenger in eukaryotic cells, associated with cellular functions such as cell cycle regulation, transport, motility, gene expression, and regulation. The use of fluorometric techniques in isolated cells loaded with Ca2+-sensitive fluorescent probes allows quantitative measurement of dynamic events occurring in living, functioning cells. The Cardiomyocytes Images Analyzer Python (CardIAP) application addresses the need to analyze and retrieve information from confocal microscopy images systematically, accurately, and rapidly. Here we present CardIAP, an open-source tool developed entirely in Python, freely available and useable in an interactive web application. In addition, CardIAP can be used as a standalone Python library and freely installed via PIP, making it easy to integrate into biomedical imaging pipelines. The images that can be generated in the study of the heart have the particularity of requiring both spatial and temporal analysis. CardIAP aims to open the field of cardiomyocytes and intact hearts image processing. The improvement in the extraction of information from the images will allow optimizing the usage of resources and animals. With CardIAP, users can run the analysis to both, the complete image, and portions of it in an easy way, and replicate it on a series of images. This analysis provides users with information on the spatial and temporal changes in calcium releases and characterizes them. The web application also allows users to extract calcium dynamics data in downloadable tables, simplifying the calculation of alternation and discordance indices and their classification. CardIAP aims to provide a tool that could assist biomedical researchers in studying the underlying mechanisms of anomalous calcium release phenomena.

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Mesmerize: a dynamically adaptable user-friendly analysis platform for 2D & 3D calcium imaging data

Cited by 5 publications

References 85 publications

Mapping calcium dynamics in a developing tubular structure

Mapping calcium dynamics in a developing tubular structure

Transitions of motor neuron activities during Ciona development

CardIAP: calcium transients confocal image analysis tool

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