CeLaVi: An Interactive Cell Lineage Visualisation Tool
Preprint posted on 15 December 2020 https://www.biorxiv.org/content/10.1101/2020.12.14.422765v1
Article now published in Nucleic Acids Research at http://dx.doi.org/10.1093/nar/gkab325
The development of multicellular organisms starts from single cells that undergo a coordinated process of cell division, morphogenesis and cell differentiation. Cell divisions constitute a genealogical tree, which can provide a framework for understanding how and when cell fate decisions are made. Cell lineage visualization has relied on following successive cell divisions of developing organisms under the microscope. Recent developments in imaging technologies have simplified this process, making it possible to image larger numbers of cells at a time. In parallel, genetic lineage recorders have been developed, which make it possible to reconstruct the entire lineage history of a complex organism. A complex goal, however, is to integrate the description of cell relationships with information about the spatial distribution and identities of the cells those divisions produce. It is not uncommon in biology, however, that as technologies are developed allowing further investigation of biological phenomena, the software to handle vast amounts of data lags behind. To bridge this gap, in their work, Salvador-Martinez et al (1) present CeLaVi (Cell Lineage Visualization tool), which is a web-based tool that allows users to navigate and explore cell lineage while also making it possible to visualize the spatial distribution, identities and properties of cells. Moreover, it allows 3D viewing and annotation of various cell qualities, including gene expression, cell type and tissue layer. They present this software as open-source, with example datasets and video tutorials http://www.celavi.pro.
Key findings and developments
Developments. CeLaVi is built using HTML5, Ajax, jQuery, CSS and the visualization libraries D3.js and Plotly.js. It was tested in multiple operating systems (Linux, MacOS, Windows) and browsers (Chrome, Firefox, Safari). The user interface consists of two interactive spaces: the lineage viewer, and the 3D viewer, which are tightly integrated. The users can explore various features including visualizing individual branches of the cell lineage tree, exploring the spatial distribution of cells in 3D, visualizing the spatial distribution of cell clones, selecting cells to display their lineage history, and visualizing the clonal relationship of any cell to others in 3D. To visualize a cell lineage tree and relate it to a 3D representation of the positions of each cell, two files are required: one containing the lineage tree, and one containing the 3D coordinates of the same cells.
The authors then describe in detail the two viewers, with the following key points:
Lineage tree viewer. CeLaVi’s lineage tree viewer can accommodate very large trees while retaining tree legibility. The viewer allows the user to focus on specific branches of the lineage tree by expanding, collapsing or pruning selected branches. Interacting with each cell in the lineage tree can provide specific cell information, for instance, cell ID, and total number of descendants.
3D viewer. CeLaVi’s 3D viewer renders cells as spheres, which users can interact with. It allows visualizing the degree of lineage relationship of all cells relative to one selected cell, showing the nested set of clones to which the cell belongs.
Information visualization. CeLaVi allows visualizing cell clones, and multiple clones originating at a given tree depth can be simultaneously visualized with unique colour coding. The software allows users to save selected cells or cell clones with customized annotations. The software allows two important pieces of further information to be uploaded and associated with the two viewer windows, namely, cell type information (a file containing cell annotations), and gene expression data, to see relative expression levels of a gene of interest.
The authors then include 4 example datasets in which they demonstrate CeLaVi’s features. These include a) C. elegans L1 larva including information from previous studies, on 357 cells viewed using confocal microscopy; b) Ciona intestinalis gastrula combining previously available 3D imaging and gene expression data; c) Parhyale hawaiensis limb, including previously available data from fluorescently-labeled embryos imaged with multi-view light-sheet microscopy at high spatiotemporal resolution over several days of embryogenesis; d) in silico organoid, from a simulation of morphogenesis.
Altogether, the authors present CeLaVi as the first interactive web-based visualization tool for cell lineages, with simple representations of that enables fast rendering in 3D, which is key for data exploration.
What I like about this paper
I like this preprint for three key things: first, that usually software lags behind technological advances that make certain types of experiments possible, which usually results in analysis being challenging for some time, until the relevant software tools catch up and allow it. I like that the authors bridge this gap here. The second reason is that I like the principles of open science and open access, and here the authors make their tool available to the scientific community. Not only that, but it is web-based and simple to use, translating as greater accessibility. Finally, the title is great!
- Salvador-Martinez et al, CeLaVi: an interactive cell lineage visualization tool, bioRxiv, 2020.
Posted on: 23 December 2020Read preprint
Also in the cell biology category:
Invasion of glioma cells through confined space requires membrane tension regulation and mechano-electrical coupling via Plexin-B2
Excitable Rho dynamics drive cell contractions by sequentially inducing ERM protein-mediated actin-membrane attachment and actomyosin contractility
Nanos2+ cells give rise to germline and somatic lineages in the sea anemone Nematostella vectensis
preListscell biology category:in the
‘In preprints’ from Development 2022-2023
A list of the preprints featured in Development's 'In preprints' articles between 2022-2023
|Alex Eve, Katherine Brown
preLights peer support – preprints of interest
This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.
|preLights peer support
The Society for Developmental Biology 82nd Annual Meeting
This preList is made up of the preprints discussed during the Society for Developmental Biology 82nd Annual Meeting that took place in Chicago in July 2023.
|Joyce Yu, Katherine Brown
CSHL 87th Symposium: Stem Cells
Preprints mentioned by speakers at the #CSHLsymp23
Journal of Cell Science meeting ‘Imaging Cell Dynamics’
This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
Alumni picks – preLights 5th Birthday
This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.
|Sergio Menchero et al.
CellBio 2022 – An ASCB/EMBO Meeting
This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.
|Nadja Hümpfer et al.
The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
Planar Cell Polarity – PCP
This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.
BioMalPar XVI: Biology and Pathology of the Malaria Parasite
[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria
|Dey Lab, Samantha Seah
Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
|Maiko Kitaoka et al.
A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.
|Paul Gerald L. Sanchez and Stefano Vianello
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
|Madhuja Samaddar et al.
EMBL Seeing is Believing – Imaging the Molecular Processes of Life
Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019
Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.
|Sandra Malmgren Hill
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.
|Pablo Ranea Robles
BSCB/BSDB Annual Meeting 2019
Preprints presented at the BSCB/BSDB Annual Meeting 2019
This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.
|Sandra Franco Iborra
Biophysical Society Annual Meeting 2019
Few of the preprints that were discussed in the recent BPS annual meeting at Baltimore, USA
|Joseph Jose Thottacherry
ASCB/EMBO Annual Meeting 2018
This list relates to preprints that were discussed at the recent ASCB conference.
|Dey Lab, Amanda Haage