Limits...
Object-based representation and analysis of light and electron microscopic volume data using Blender.

Asadulina A, Conzelmann M, Williams EA, Panzera A, Jékely G - BMC Bioinformatics (2015)

Bottom Line: We also represent and analyze connectome data including neuronal reconstructions and underlying synaptic connectivity.The resources we have developed for Platynereis will facilitate data sharing and the standardization of anatomical atlases for this species.The flexibility of Blender, particularly its embedded Python application programming interface, means that our methods can be easily extended to other organisms.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany. albina.asadulina@tuebingen.mpg.de.

ABSTRACT

Background: Rapid improvements in light and electron microscopy imaging techniques and the development of 3D anatomical atlases necessitate new approaches for the visualization and analysis of image data. Pixel-based representations of raw light microscopy data suffer from limitations in the number of channels that can be visualized simultaneously. Complex electron microscopic reconstructions from large tissue volumes are also challenging to visualize and analyze.

Results: Here we exploit the advanced visualization capabilities and flexibility of the open-source platform Blender to visualize and analyze anatomical atlases. We use light-microscopy-based gene expression atlases and electron microscopy connectome volume data from larval stages of the marine annelid Platynereis dumerilii. We build object-based larval gene expression atlases in Blender and develop tools for annotation and coexpression analysis. We also represent and analyze connectome data including neuronal reconstructions and underlying synaptic connectivity.

Conclusions: We demonstrate the power and flexibility of Blender for visualizing and exploring complex anatomical atlases. The resources we have developed for Platynereis will facilitate data sharing and the standardization of anatomical atlases for this species. The flexibility of Blender, particularly its embedded Python application programming interface, means that our methods can be easily extended to other organisms.

No MeSH data available.


Pipeline for generating a model of a gene expression atlas. An individual gene expression pattern is thresholded and converted into a surface representation using the ImageJ plugin 3D Viewer. The surfaces are then exported from 3D Viewer in OBJ format and imported in Blender. Scale bar 30 μm
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4513682&req=5

Fig1: Pipeline for generating a model of a gene expression atlas. An individual gene expression pattern is thresholded and converted into a surface representation using the ImageJ plugin 3D Viewer. The surfaces are then exported from 3D Viewer in OBJ format and imported in Blender. Scale bar 30 μm

Mentions: Platynereis larvae are amenable to near cellular-resolution expression profiling using in situ hybridization and gene expression atlases [33, 34]. However, the number of genes that can be simultaneously displayed in an atlas has been limited. We used Blender to efficiently visualize and analyze gene expression atlases for three Platynereis larval stages (48 hours post fertilization (hpf), 72 hpf, 6 days post fertilization (dpf)). The atlases were generated by registering gene expression patterns to stage-specific average nuclear-stain (DAPI) templates [34]. For each gene we calculated an average expression pattern, which, following thresholding, was imported into Blender (Fig. 1). To provide an anatomical reference, we also imported an average acetylated tubulin immunostaining signal that labels cilia, axons and dendrites within the larvae. The surface representation used by Blender allows fast 3D visualization for several channels, a feature that is limited in pixel-based visualization methods (Fig. 2).Fig. 1


Object-based representation and analysis of light and electron microscopic volume data using Blender.

Asadulina A, Conzelmann M, Williams EA, Panzera A, Jékely G - BMC Bioinformatics (2015)

Pipeline for generating a model of a gene expression atlas. An individual gene expression pattern is thresholded and converted into a surface representation using the ImageJ plugin 3D Viewer. The surfaces are then exported from 3D Viewer in OBJ format and imported in Blender. Scale bar 30 μm
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4513682&req=5

Fig1: Pipeline for generating a model of a gene expression atlas. An individual gene expression pattern is thresholded and converted into a surface representation using the ImageJ plugin 3D Viewer. The surfaces are then exported from 3D Viewer in OBJ format and imported in Blender. Scale bar 30 μm
Mentions: Platynereis larvae are amenable to near cellular-resolution expression profiling using in situ hybridization and gene expression atlases [33, 34]. However, the number of genes that can be simultaneously displayed in an atlas has been limited. We used Blender to efficiently visualize and analyze gene expression atlases for three Platynereis larval stages (48 hours post fertilization (hpf), 72 hpf, 6 days post fertilization (dpf)). The atlases were generated by registering gene expression patterns to stage-specific average nuclear-stain (DAPI) templates [34]. For each gene we calculated an average expression pattern, which, following thresholding, was imported into Blender (Fig. 1). To provide an anatomical reference, we also imported an average acetylated tubulin immunostaining signal that labels cilia, axons and dendrites within the larvae. The surface representation used by Blender allows fast 3D visualization for several channels, a feature that is limited in pixel-based visualization methods (Fig. 2).Fig. 1

Bottom Line: We also represent and analyze connectome data including neuronal reconstructions and underlying synaptic connectivity.The resources we have developed for Platynereis will facilitate data sharing and the standardization of anatomical atlases for this species.The flexibility of Blender, particularly its embedded Python application programming interface, means that our methods can be easily extended to other organisms.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany. albina.asadulina@tuebingen.mpg.de.

ABSTRACT

Background: Rapid improvements in light and electron microscopy imaging techniques and the development of 3D anatomical atlases necessitate new approaches for the visualization and analysis of image data. Pixel-based representations of raw light microscopy data suffer from limitations in the number of channels that can be visualized simultaneously. Complex electron microscopic reconstructions from large tissue volumes are also challenging to visualize and analyze.

Results: Here we exploit the advanced visualization capabilities and flexibility of the open-source platform Blender to visualize and analyze anatomical atlases. We use light-microscopy-based gene expression atlases and electron microscopy connectome volume data from larval stages of the marine annelid Platynereis dumerilii. We build object-based larval gene expression atlases in Blender and develop tools for annotation and coexpression analysis. We also represent and analyze connectome data including neuronal reconstructions and underlying synaptic connectivity.

Conclusions: We demonstrate the power and flexibility of Blender for visualizing and exploring complex anatomical atlases. The resources we have developed for Platynereis will facilitate data sharing and the standardization of anatomical atlases for this species. The flexibility of Blender, particularly its embedded Python application programming interface, means that our methods can be easily extended to other organisms.

No MeSH data available.