Biology subjects

Chen, T.-W.

Publications and source records attributed to Chen, T.-W..

4 recordsLinked to original sources

bioRxiv2019

A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology

Calcium imaging with fluorescent protein sensors is widely used to record activity in neuronal populations. The transform between neural activity and calcium-related fluorescence involves nonlinearities and a low-pass filter, but the effects of the transformation on analyses of neural populations are not well understood. We compared neuronal spikes and fluorescence in matched neural populations in behaving mice. We report multiple discrepancies between analyses performed on the two types of data, which were only partially resolved by spike inference algorithms applied to fluorescence. To model the relation between spiking and fluorescence we simultaneously recorded spikes and fluorescence from individual neurons. Using these recordings we developed a model transforming spike trains to synthetic-imaging data. The model recapitulated the differences in analyses. Our analysis highlights challenges in relating electrophysiology and imaging data, and suggests forward modeling as an effective way to understand differences between these data.

neuroscience↗

bioRxiv2019

Phenomenal: An automatic open source library for 3D shoot architecture reconstruction and analysis for image-based plant phenotyping

In the era of high-throughput visual plant phenotyping, it is crucial to design fully automated and flexible workflows able to derive quantitative traits from plant images. Over the last years, several software supports the extraction of architectural features of shoot systems. Yet currently no end-to-end systems are able to extract both 3D shoot topology and geometry of plants automatically from images on large datasets and a large range of species. In particular, these software essentially deal with dicotyledons, whose architecture is comparatively easier to analyze than monocotyledons. To tackle these challenges, we designed the Phenomenal software featured with: (i) a completely automatic workflow system including data import, reconstruction of 3D plant architecture for a range of species and quantitative measurements on the reconstructed plants; (ii) an open source library for the development and comparison of new algorithms to perform 3D shoot reconstruction and (iii) an integration framework to couple workflow outputs with existing models towards model-assisted phenotyping. Phenomenal analyzes a large variety of data sets and species from images of high-throughput phenotyping platform experiments to published data obtained in different conditions and provided in a different format. Phenomenal has been validated both on manual measurements and synthetic data simulated by 3D models. It has been also tested on other published datasets to reproduce a published semi-automatic reconstruction workflow in an automatic way. Phenomenal is available as an open-source software on a public repository.

plant biology↗

bioRxiv2019

The RNA Atlas, a single nucleotide resolution map of the human transcriptome

The human transcriptome consists of various RNA biotypes including multiple types of non-coding RNAs (ncRNAs). Current ncRNA compendia remain incomplete partially because they are almost exclusively derived from the interrogation of small- and polyadenylated RNAs. Here, we present a more comprehensive atlas of the human transcriptome that is derived from matching polyA-, total-, and small-RNA profiles of a heterogeneous collection of nearly 300 human tissues and cell lines. We report on thousands of novel RNA species across all major RNA biotypes, including a hitherto poorly-cataloged class of non-polyadenylated single-exon long non-coding RNAs. In addition, we exploit intron abundance estimates from total RNA-sequencing to test and verify functional regulation by novel non-coding RNAs. Our study represents a substantial expansion of the current catalogue of human ncRNAs and their regulatory interactions. All data, analyses, and results are available in the R2 web portal and serve as a basis to further explore RNA biology and function.

genetics↗

bioRxiv2018

Bright and photostable chemigenetic indicators for extended in vivo voltage imaging

Imaging changes in membrane potential using genetically encoded fluorescent voltage indicators (GEVIs) has great potential for monitoring neuronal activity with high spatial and temporal resolution. Brightness and photostability of fluorescent proteins and rhodopsins have limited the utility of existing GEVIs. We engineered a novel GEVI, Voltron, that utilizes bright and photostable synthetic dyes instead of protein-based fluorophores, extending the combined duration of imaging and number of neurons imaged simultaneously by more than tenfold relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously, over 15 minutes of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.

neuroscience↗