Exploring spatio-temporal dynamics of gene expression using Transmodal Registration
Manan Lalit
(Jug & Tomancak Labs)
Dynamic changes in gene expression occur during early development
Embryo at 16 hpf*
Embryo at 20 hpf
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* hours post fertilization
Dynamic changes in gene expression occur during early development
Embryo at 16 hpf*
Embryo at 20 hpf
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* hours post fertilization
Building lineage trees with gene expression data requires bringing two datasets together
Live Embryo imaged with Light Sheet Microscopy: Nuclei, Membrane
In-situ Specimen at 16 hpf imaged with Confocal Microscopy: Nuclei, Pax3/7
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Image Registration holds the answer
- Intensity or Feature based
- Global Transform based on Linear Models, Local Transform based on Non-Linear, Elastic Models
Add Image
In-situ specimens for 50 genes at 3 developmental stages were imaged
Mette Handberg-Thorsager
Live imaging & tracking for three embryos was performed
Mette Handberg-Thorsager
Locations and size of cell nuclei from in-situ specimens were extracted
Feature Detection with Automatic Scale Selection, Lindeberg, T., International Journal of Computer Vision
Live Embryo: Nuclei. Cell nuclei positions were fitted to an ellipsoid
In-situ Specimen: Nuclei. Cell nuclei positions were fitted to an ellipsoid
Fixation introduces shrinking of the embryo
Choosing a few corresponding nuclei helps to recover the scale, orientation and translation
Live Embryo: Nuclei, Membrane
In-situ Specimen: Nuclei
Choosing a few corresponding voxels helps to recover the scale, orientation and translation
Live Embryo: Nuclei
In-situ Specimen after transformation: Nuclei
In-situ Specimen before transformation: Nuclei
The number of cell nuclei is used as a measure for staging the in-situ specimen
Number of cell nuclei in in-situ specimens at 16 and 20 hpf
Selection of the correct time point is based on one-to-one mapping
Lineage trees with gene expression data would allow cellular resolution, co-expression studies
In-situ Specimen imaged with Confocal Microscopy: Nuclei, pax3/7
In-situ Specimen imaged with Confocal Microscopy: Nuclei, pax6
Co-expression (Max z-projection ), obtained using ProSPr *
* Whole-organism cellular gene expression atlas, Vergara et al,
Initial Results
Pax 3/7 @ 16 and 20 hpf
SimViewer Video
Mastodon GIF
Future: By-passing the hand-picking of corresponding voxels
Future: Adding Single Cell RNA-Sequencing data to the mix
Developmental Cell Lineage
Mette Handberg-Thorsager
Mette Handberg-Thorsager
Thank you for listening! Any questions?
Tomancak Lab
Marina Cuenca
Johannes Girstmair
Pavel Mejstrik
Stefan Münster
Giulia Serafini
Mette Handberg-Thorsager
Gabriella Turek
Vladimir Ulman
Bruno Cossermelli Vellutini
Jug Lab Tim-Oliver Buccholz Alexander Krull Mangal Prakash Deborah Schmidt
Jug/ Zechner Lab
Tobias Pietzsch
Jug/ Honigmann Lab
Anna Goncharova
Jug/ Zerial Lab
Nuno Pimpao Martins
Myers Lab
Matthias Arzt
Traversing across the lineage tree allows generating a virtual atlas to study co-expression
Cyan: Nuclei of Fixed Image # 1
Magenta: Nuclei of Fixed Image # 2
Averaged Atlas at 20 hpf (generated using ProSPr*)
* Whole-organism cellular gene expression atlas, Vergara et al,
Friday Seminar
By Manan Lalit
