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

This is the final version of the article. Available from the publisher via the DOI in this record.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.The research leading to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/European Research Council Grant Agreement 260821

Tomographic diffractive microscopy: towards highresolution 3-D real-time data acquisition, image reconstruction and display of unlabeled samples

Tomographic diffractive microscopy allows for imaging unlabeled specimens, with a better resolution than conventional microscopes, giving access to the index of refraction distribution within the specimen, and possibly at high speed. Principles of image formation and reconstruction are presented, and progresses towards realtime, three-dimensional acquisition, image reconstruction and final display, are discussed

Desenvolvimento de uma interface de visualização de conectividade cerebral usando realidade virtual e controlo por gestos

A presente dissertação foi desenvolvida em colaboração com o Instituto de Biofísica e Engenharia Biomédica(IBEB/FCUL)A visualização de dados médicos complexos, em particular de dados imagiológicos, de forma intuitiva, simples e completa é um desafio. Com as tecnologias de aquisição de imagem médica usadas atualmente é possível ter acesso a um vasto leque de informação relevante para diagnóstico e tratamento de patologias. Assim sendo, é fundamental que a visualização dessa mesma informação seja feita de uma forma rápida e intuitiva. No presente trabalho desenvolveu-se uma nova ferramenta de visualização de imagens de ressonância magnética e de conectividade cerebral. Esta ferramenta contém em si uma interface amigável e intuitiva para o utilizador, fazendo uso de duas tecnologias emergentes, a realidade virtual e o reconhecimento gestual. No desenvolvimento da interface fez-se ainda uso de uma tecnologia menos usual na área médica, a Game Engine Unity 3D,usada convencionalmente na programação de jogos de vídeo. A interface oferece um ambiente imersivo 3D da anatomia e conectividade cerebrais, fazendo uso de óculos de realidade virtual. Nesta interface o utilizador consegue navegar no interior no cérebro, fazendo uma interação com as estruturas com recurso ao controlo do Leap Motion, um dispositivo ótico de reconhecimento gestual. Esta interface de "navegação cerebral" será útil no futuro para a comunidade médica, em particular para a formação de neurocirurgiões graças ao reconhecimento gestual. Além disso, a interface fornece informações sobre as estruturas cerebrais e vários parâmetros de dados de imagens e de conectividade cerebral, tornando-se adequada para o ensino e investigação em neurociências.Fundação para a Ciência e a Tecnologia (FCT)e Ministério da Ciência e Educação (MCE) Portugal (PIDDAC) integrado nos projetos PTDC/SAU-ENB/120718/2010 e PEst-OE/SAU/UI0645/201

The evolution of shell form in tropical terrestrial microsnails

Mollusca form an important animal phylum that first appeared in the Cambrian, and today is,after Arthropoda, the second largest animal phylum, with more than 100,000 extant species(Bieler, 1992, Brusca and Brusca, 2003), with the class Gastropoda accounting for 80% of the extant species in the Mollusca. Despite its species-richness, a generalised gastropod shell architecture is maintained because of conserved developmental processes. All of the shelled gastropods grow by adding, in a unidirectional accretionary way, shell material with the mantle edge organ, usually at different deposition rates around the existing aperture. This shell ontogeny, or to be more specific aperture ontogeny, gives the general spiral form for the shells. However, spiral forms can vary when there are changes in any one of the aspects in the aperture ontogeny profiles, namely, the rate and direction of shell deposition around the aperture, size and shape of the aperture (i.e. mantle edge), and the total length of the shell ontogeny processes. The interplays between these developmental parameters have generated a great diversity in shell form, for which taxonomists and evolutionary biologist are now trying to accurately characterise and to understand with regard to its evolution.This thesis reveals several hitherto unknown aspects of Plectostoma shell forms,in terms of the developmental homology, the aperture ontogeny profile, anti-predation functionality, and evolutionary pattern in shell characters and ontogenetic morphospace evolution. In fact, these are the issues that have been targeted by biologists for centuries in order to improve the way shell shape is characterised and to improve understanding of shell form evolution.he research presented in this thesis was supported by the Netherlands Organization for Scientific Research (NWO, grant no. 819.01.012).UBL - phd migration 201