Multiscale light-sheet organoid imaging framework
Posted on: 29 August 2021 , updated on: 1 September 2021
Preprint posted on 12 May 2021
Article now published in Nature Communications at http://dx.doi.org/10.1038/s41467-022-32465-z
Categories: biochemistry, bioengineering, cell biology, developmental biology
Background
Organoids, multicellular in vitro models of their corresponding organs, are an excellent resource for understanding the cellular and developmental mechanisms that regulate tissue and organ growth. In recent years, organoids have relieved some of the difficulties and complexities of working with organs in vivo. Intestinal organoids are a great example of a reproducible system capable of recapitulating not only major morphological features (e.g., crypt formation) [1] but also one of the major intestine capabilities — its regenerative response [2].
One advantage of working with organoids is that their development can be precisely followed under a microscope, potentially allowing the description of their cells’ genealogical tree or lineage. However, imaging and analyzing organoid growth remains challenging, as it requires long-term imaging microscopy techniques coupled with cell-tracking and dedicated analysis pipelines to recover morphological or cell lineage information.
In this exciting new preprint, Liberali and colleagues leverage their extensive organoid-imaging knowledge [3] to present LSTree (an acronym for Light-Sheet Tree), a light-sheet imaging framework to analyze and digitally visualize organoids. LST goes from image pre-processing, cell lineage tracking, and segmentation to analytical tools to extract morphological and microscopy features. The authors used this light-sheet microscopy-based imaging framework to analyze and reconstruct, at an unprecedented spatiotemporal resolution, the cell growing dynamics and cell lineage relationships during intestinal organoid development.
About the preprint
Imaging framework
Medeiros et al. took advantage of the abundance of knowledge on intestinal organoids and used it to provide quantitative information on intestinal organoid growth dynamics using light-sheet and spinning disk microscopy.
The authors based their initial work on previously published protocols for imaging organoids, using cultured mouse intestinal crypt organoids and single-cell dissociation, followed by fluorescent-activated cell sorting (FACS) and embedding into a Matrigel drop. Hence, organoid-derived single cells were cultured into a sample holder specially designed for light-sheet imaging using a dual-illumination inverted light-sheet microscope. In addition, the authors developed a position-dependent illumination alignment step to obtain the best image quality possible. Aiming to reduce the storage needs, the authors compressed and cropped the images. The low signal-to-noise ratio, due to the very low laser intensity to avoid phototoxicity, was improved by denoising and deconvoluting the images.
To track and record the cell and cell lineages, Medeiros et al. worked with intestinal organoid-derived cells expressing the nuclear Histone 2B and mem9 membrane peptide, each tagged with fluorescent proteins (Fig. 1). Then, the authors recorded the time-lapse growth of the intestinal organoids every 10 min for about four days to study the individual cell dynamics by semi-automated tracking and single-cell segmentation. Owing to the 3D spatiotemporal dissection of the intestinal cellular dynamics, the authors were able to extract 3D information and plot the data over this time period, shedding light on cell division, cell and nucleus volume, and density, as well as cell changes induced by the daily media changes. Remarkably, they found nuclei volume decreased with each cell locating more distantly to the organoid lumen with each LSTree generation.
Fig. 1. Light-sheet high-resolution imaging framework. Modified from Medeiros et al. 2021.
Deep learning 4D organoid segmentation and multiscale digital viewer
With their protocol established, the authors added their image processing and data analyses into LSTree (for details visit: https://github.com/fmi-basel/LSTree), which was implemented as a Luigi (i.e., a workflow engine) (https://github.com/spotify/luigi). The next challenge was to perform organoid segmentation with their framework. The authors introduced a number of different segmentation strategies for organoid segmentation (cells and nuclei) that use convolutional neural networks and a trained deep learning model. Using this strategy, they extracted several distinct features from the organoid cells. Continuing with the framework development, Medeiros et al. trained and refined a deep learning model together with developing a segmentation-tracking approach to map the association between nuclei in two consecutive frames in 4D. With this achieved, the authors created a digital organoid viewer to facilitate data exploration. Remarkably, the viewer combines lineage cell trees and cell meshes, representing a multiscale organoid digital web-viewer (Fig. 2).
Fig. 2. Highlights of the organoid digital viewer developed by the authors.
Functional imaging through fixation and backtracking
Aiming to address the end state of the organoid cells and to overcome several problems involved with imaging multiple fluorescent organoid lines (i.e., reporter lines), the authors included fixation and immunolabelling as the last step after the recording. Following live recording, they integrated fixation and immunofluorescence to detect the cells expressing their proteins of interest. Hence, post-fixation staining of DLL1 (also known as Delta-like ligand 1 precursor, a marker for secretory lineage cells) and Lysozyme (a marker for differentiated Paneth cells) allowed the authors to ask about symmetry breaking of the intestinal organoid. Of note, the authors also calculated that on average an organoid cell has 5 closest neighbors. Thus, the authors were able to image and backtrack the stained cells with the light-sheet live recordings, enhancing the discovery capabilities of LSTree.
Polyploidy events during early gut organoid development
A challenging observation was that some cells went through a few rounds of failed cell division, meaning that two sister nuclei divided into two instead of four nuclei at the end of their cell cycle. The authors showed that the cause of these failed division events was an issue during cytokinesis. Interestingly, the organoids seem to exclude these cytokinesis failure events from the crypt, but a high proportion of the “failed” cell progeny localized to the villus. Thus, the authors proposed that the organoid system possesses an intrinsic self-preserving mechanism by avoiding cell division failure or damaged cells within the crypt – something they speculate could also occur in the gut. To finish, Medeiros et al. showed that LATS1 and YAP participate in regulating successful mitosis and cytokinesis, whereas perturbations of these resulted in inefficient mitosis and cell division.
What I liked about this preprint
This impressive multivariate and multiscale analytical framework was applied from a single cell to hundreds of cells and encompassed image pre-processing, lineage tracking, and segmentation coupled with analytical tools. Therefore, LSTree allowed the researchers to extract single-cell morphological features in 4D. In addition to developing a light-sheet microscopy pipeline combined with a web-based “digital organoid viewer”, the authors proposed a model of tissue development and integrity maintenance that challenges the concept of polyploidy in tissue homeostasis and regeneration. This remarkable approach will open new avenues in our understanding of organoid development and might allow further multi-parametric functional characterization of different organoid growth.
Future directions and questions to the authors
- Is there any potential for combining your LSTree approach with spatial transcriptomics?
- Have you applied this light-sheet imaging strategy and LSTree to study other kinds of organoids? I wonder whether other tissue-specific organoids might represent hurdles and challenges to further test LSTree applicability and feasibility.
- What was the most challenging aspect of creating LSTree?
- Have you explored the roles of YAP-mediated mechanotransduction or ECM/nuclear mechanotransduction of YAP as regulators of successful cell division/cytokinesis? Any thoughts if not explored yet?
Acknowledgments
Osvaldo Contreras acknowledges Irepan Salvador for initial discussions of the Medeiros et al. preprint and Helen Robertson for valuable comments on this PreLight.
References
[1] Serra, D., Mayr, U., Boni, A. et al. Self-organization and symmetry breaking in intestinal organoid development. Nature 569, 66–72 (2019). https://doi.org/10.1038/s41586-019-1146-y
[2] Lukonin, I., Serra, D., Challet Meylan, L. et al. Phenotypic landscape of intestinal organoid regeneration. Nature 586, 275–280 (2020). https://doi.org/10.1038/s41586-020-2776-9
[3] Yang, Q., Xue, SL., Chan, C.J. et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nat Cell Biol 23, 733–744 (2021). https://doi.org/10.1038/s41556-021-00700-2
doi: https://doi.org/10.1242/prelights.30401
Read preprint
(2 votes) Have your say
Sign up to customise the site to your preferences and to receive alerts
Register hereAlso in the biochemistry category:
Triglyceride metabolism controls inflammation and APOE4-associated disease states in microglia
Gustavo Stelzer, Marcus Oliveira
Impaired 26S proteasome causes learning and memory deficiency and induces neuroinflammation mediated by NF-κB in mice
Gustavo Stelzer, Marcus Oliveira
Notch3 is a genetic modifier of NODAL signalling for patterning asymmetry during mouse heart looping
Bhaval Parmar
Also in the bioengineering category:
Green synthesized silver nanoparticles from Moringa: Potential for preventative treatment of SARS-CoV-2 contaminated water
Safieh Shah, Benjamin Dominik Maier
Engineered Nanotopographies Induce Transient Openings in the Nuclear Membrane
Sristilekha Nath
Scalable and efficient generation of mouse primordial germ cell-like cells
Carly Guiltinan
Also in the cell biology category:
Restoring mechanophenotype reverts malignant properties of ECM-enriched vocal fold cancer
Teodora Piskova
Germplasm stability in zebrafish requires maternal Tdrd6a and Tdrd6c
Justin Gutkowski
Leukocytes use endothelial membrane tunnels to extravasate the vasculature
Felipe Del Valle Batalla
Also in the developmental biology category:
Germplasm stability in zebrafish requires maternal Tdrd6a and Tdrd6c
Justin Gutkowski
Cellular signalling protrusions enable dynamic distant contacts in spinal cord neurogenesis
Ankita Walvekar
Actin-based deformations of the nucleus control multiciliated ependymal cell differentiation
Ryan Harrison
preLists in the biochemistry category:
BSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
| List by | Reinier Prosee |
Peer Review in Biomedical Sciences
Communication of scientific knowledge has changed dramatically in recent decades and the public perception of scientific discoveries depends on the peer review process of articles published in scientific journals. Preprints are key vehicles for the dissemination of scientific discoveries, but they are still not properly recognized by the scientific community since peer review is very limited. On the other hand, peer review is very heterogeneous and a fundamental aspect to improve it is to train young scientists on how to think critically and how to evaluate scientific knowledge in a professional way. Thus, this course aims to: i) train students on how to perform peer review of scientific manuscripts in a professional manner; ii) develop students' critical thinking; iii) contribute to the appreciation of preprints as important vehicles for the dissemination of scientific knowledge without restrictions; iv) contribute to the development of students' curricula, as their opinions will be published and indexed on the preLights platform. The evaluations will be based on qualitative analyses of the oral presentations of preprints in the field of biomedical sciences deposited in the bioRxiv server, of the critical reports written by the students, as well as of the participation of the students during the preprints discussions.
| List by | Marcus Oliveira 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.
| List by | Nadja Hümpfer et al. |
20th “Genetics Workshops in Hungary”, Szeged (25th, September)
In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf
| List by | Nándor Lipták |
Fibroblasts
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!
| List by | Osvaldo Contreras |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
| List by | 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
| List by | Dey Lab |
Cellular metabolism
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.
| List by | Pablo Ranea Robles |
MitoList
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.
| List by | Sandra Franco Iborra |
Also in the bioengineering category:
CSHL 87th Symposium: Stem Cells
Preprints mentioned by speakers at the #CSHLsymp23
| List by | Alex Eve |
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
| List by | Alex Eve |
3D Gastruloids
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.
| List by | Paul Gerald L. Sanchez and Stefano Vianello |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
| List by | 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
| List by | Dey Lab |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
| List by | Rob Hynds |
Advances in microscopy
This preList highlights exciting unpublished preprint articles describing advances in microscopy with a focus on light-sheet microscopy.
| List by | Stephan Daetwyler |
Also in the cell biology category:
November in preprints – the CellBio edition
This is the first community-driven preList! A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. Categories include: 1) cancer cell biology 2) cell cycle and division 3) cell migration and cytoskeleton 4) cell organelles and organisation 5) cell signalling and mechanosensing 6) genetics/gene expression
| List by | Felipe Del Valle Batalla et al. |
BSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
| List by | Reinier Prosee |
‘In preprints’ from Development 2022-2023
A list of the preprints featured in Development's 'In preprints' articles between 2022-2023
| List by | 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.
| List by | 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.
| List by | Joyce Yu, Katherine Brown |
CSHL 87th Symposium: Stem Cells
Preprints mentioned by speakers at the #CSHLsymp23
| List by | Alex Eve |
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.
| List by | Helen Zenner |
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.
| List by | Martin Estermann |
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.
| List by | 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.
| List by | Nadja Hümpfer et al. |
Fibroblasts
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!
| List by | Osvaldo Contreras |
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
| List by | Alex Eve |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
| List by | Ana Dorrego-Rivas |
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.
| List by | Ana Dorrego-Rivas |
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
| List by | Dey Lab, Samantha Seah |
1
Cell Polarity
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.
| List by | Yamini Ravichandran |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
| List by | Maiko Kitaoka et al. |
3D Gastruloids
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.
| List by | Paul Gerald L. Sanchez and Stefano Vianello |
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
| List by | Hiral Shah |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
| List by | 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
| List by | Dey Lab |
Autophagy
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.
| List by | Sandra Malmgren Hill |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
| List by | Rob Hynds |
Cellular metabolism
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.
| List by | Pablo Ranea Robles |
BSCB/BSDB Annual Meeting 2019
Preprints presented at the BSCB/BSDB Annual Meeting 2019
| List by | Dey Lab |
MitoList
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.
| List by | Sandra Franco Iborra |
Biophysical Society Annual Meeting 2019
Few of the preprints that were discussed in the recent BPS annual meeting at Baltimore, USA
| List by | Joseph Jose Thottacherry |
ASCB/EMBO Annual Meeting 2018
This list relates to preprints that were discussed at the recent ASCB conference.
| List by | Dey Lab, Amanda Haage |
Also in the developmental biology category:
BSDB/GenSoc Spring Meeting 2024
A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.
| List by | Joyce Yu, Katherine Brown |
GfE/ DSDB meeting 2024
This preList highlights the preprints discussed at the 2024 joint German and Dutch developmental biology societies meeting that took place in March 2024 in Osnabrück, Germany.
| List by | Joyce Yu |
‘In preprints’ from Development 2022-2023
A list of the preprints featured in Development's 'In preprints' articles between 2022-2023
| List by | 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.
| List by | 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.
| List by | Joyce Yu, Katherine Brown |
CSHL 87th Symposium: Stem Cells
Preprints mentioned by speakers at the #CSHLsymp23
| List by | Alex Eve |
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.
| List by | Helen Zenner |
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.
| List by | Martin Estermann |
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.
| List by | 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.
| List by | Nadja Hümpfer et al. |
2nd Conference of the Visegrád Group Society for Developmental Biology
Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)
| List by | Nándor Lipták |
Fibroblasts
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!
| List by | Osvaldo Contreras |
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
| List by | Alex Eve |
EMBL Conference: From functional genomics to systems biology
Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020
| List by | Jesus Victorino |
Single Cell Biology 2020
A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.
| List by | Alex Eve |
Society for Developmental Biology 79th Annual Meeting
Preprints at SDB 2020
| List by | Irepan Salvador-Martinez, Martin Estermann |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
| List by | Ana Dorrego-Rivas |
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.
| List by | Ana Dorrego-Rivas |
Cell Polarity
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.
| List by | Yamini Ravichandran |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
| List by | Maiko Kitaoka et al. |
3D Gastruloids
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.
| List by | Paul Gerald L. Sanchez and Stefano Vianello |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
| List by | Madhuja Samaddar et al. |
EDBC Alicante 2019
Preprints presented at the European Developmental Biology Congress (EDBC) in Alicante, October 23-26 2019.
| List by | Sergio Menchero 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
| List by | Dey Lab |
SDB 78th Annual Meeting 2019
A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.
| List by | Alex Eve |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
| List by | Rob Hynds |
Young Embryologist Network Conference 2019
Preprints presented at the Young Embryologist Network 2019 conference, 13 May, The Francis Crick Institute, London
| List by | Alex Eve |
Pattern formation during development
The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.
| List by | Alexa Sadier |
BSCB/BSDB Annual Meeting 2019
Preprints presented at the BSCB/BSDB Annual Meeting 2019
| List by | Dey Lab |
Zebrafish immunology
A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.
| List by | Shikha Nayar |
3 years
Gustavo de Medeiros
Dear Osvaldo,
thank you for selecting our work for this issue of preLights!
Regarding your questions:
1) One of the things we really like about LSTree is the power of combining different data representations (lineage trees and segmented cells) within the same visualization tool, and this is one aspect that could be translated to spatial transcriptomics: to have a visualization of the RNA-seq data – e.g. via TSNE or UMAP – side by side with the corresponding imaging data. This way one could e.g. select particular cells / regions of interest from the imaging data and the corresponding points on the RNA-seq data would be highlighted, with all other properties of the cells embedded as a list of features on the RNA-seq plot, thus giving a more complete understanding of the information at hand.
2) Right now we are applying our LSTree method to other already acquired 3D+T imaging data in order to properly benchmark it and test its limits. As the recording strategy and the LSTree framework are not directly coupled, one can apply 4D datasets coming from different microscope types into the framework. The main care here is then to have good training sets for the neural networks.
3) Although tracking is one of the most basic features needed in live recorded data, most tracking approaches rely on utilizing many partial tracks in order to create lineage trees that in turn resemble an average of all of the observed systems. In our case, we needed to have trees that are 100% correct, and for that we tried to get lineage tree predictions that can avoid us having too much time on the correction / extension of these initial tracks. Turns out this fine tuning can be quite delicate depending on the data at hand, and one still needs some training sets to have a good enough network.
To facilitate this, we are now looking at ways to combine other lineage tree prediction methods to the following steps from the LSTree framewrok, making the framework more modular and open.
4) This is an interesting point, as YAP-mediated mechanotransduction or ECM/nuclear mechanotransduction of YAP may have interesting roles on the systematic appearance of mitotic defects during early organoid growth from single cells.
From looking at the recordings, during the moments where we see mitotic errors the intestinal organoids usually seem quite “malleable”, i.e. cells do not seem very stiff overall. One then could speculate that the very variability in YAP, necessary from a molecular perspective for proper symmetry breaking, might lead some cells to change their biomechanical properties to a point where cytokinesis cannot be completed. Definitely worth checking further!
Kind regards,
Gustavo