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

Dynamic changes in gene expression occur during early development

Embryo at 16 hpf*

Embryo at 20 hpf

* hours post fertilization

Building lineage trees with gene expression data requires bringing two datasets together

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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

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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, 1998 

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

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

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