Qiyuan Tian

Bio: Qiyuan Tian is an academic researcher from Harvard University. The author has contributed to research in topics: Diffusion MRI & Medicine. The author has an hindex of 16, co-authored 60 publications receiving 885 citations. Previous affiliations of Qiyuan Tian include Stanford University & Fudan University.

Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI.

Abstract: 3D histology, slice-based connectivity atlases, and diffusion MRI are common techniques to map brain wiring. While there are many modality-specific tools to process these data, there is a lack of integration across modalities. We develop an automated resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling the analysis of histological features across multiple fiber tracts and networks, and their correlation with in-vivo biomarkers. We apply our pipeline in a murine stroke model, demonstrating not only strong correspondence between MRI abnormalities and CLARITY-tissue staining, but also uncovering acute cellular effects in areas connected to the ischemic core. We provide improved maps of connectivity by quantifying projection terminals from CLARITY viral injections, and integrate diffusion MRI with CLARITY viral tracing to compare connectivity maps across scales. Finally, we demonstrate tract-level histological changes of stroke through this multimodal integration. This resource can propel investigations of network alterations underlying neurological disorders. Many approaches exist to process data from individual imaging modalities, but integrating them is challenging. The authors develop an automated resource that enables co-registered network- and tract-level analysis of macroscopic in-vivo imaging and microscopic imaging of cleared tissue.

Double diffusion encoding MRI for the clinic.

Abstract: Purpose The purpose of this study is to develop double diffusion encoding (DDE) MRI methods for clinical use. Microscopic diffusion anisotropy measurements from DDE promise greater specificity to changes in tissue microstructure compared with conventional diffusion tensor imaging, but implementation of DDE sequences on whole-body MRI scanners is challenging because of the limited gradient strengths and lengthy acquisition times. Methods A custom single-refocused DDE sequence was implemented on a 3T whole-body scanner. The DDE gradient orientation scheme and sequence parameters were optimized based on a Gaussian diffusion assumption. Using an optimized 5-min DDE acquisition, microscopic fractional anisotropy (μFA) maps were acquired for the first time in multiple sclerosis patients. Results Based on simulations and in vivo human measurements, six parallel and six orthogonal diffusion gradient pairs were found to be the minimum number of diffusion gradient pairs necessary to produce a rotationally invariant measurement of μFA. Simulations showed that optimal precision and accuracy of μFA measurements were obtained using b-values between 1500 and 3000 s/mm2 . The μFA maps showed improved delineation of multiple sclerosis lesions compared with conventional fractional anisotropy and distinct contrast from T2 -weighted fluid attenuated inversion recovery and T1 -weighted imaging. Conclusion The μFA maps can be measured using DDE in a clinical setting and may provide new opportunities for characterizing multiple sclerosis lesions and other types of tissue degeneration. Magn Reson Med 80:507-520, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Nothing in Biology Makes Sense Except in the Light of Evolution

Abstract: Nothing in biology makes sense except in the light of evolution, quipped Theodosius Dobzhansky. The theory of evolution argues that each biological species was not suddenly and independently created but that all life forms are interrelated by virtue of having descended from common ancestors through the accumulation of modifications. Indeed, nothing we know about living organisms would make any sense if they were not so interrelated. And the theory that biological species are descended from common ancestors provides an indispensable heuristic to understand why living organisms are what they are and do what they do.

Three-dimensional intact-tissue sequencing of single-cell transcriptional states.

Abstract: Retrieving high-content gene-expression information while retaining three-dimensional (3D) positional anatomy at cellular resolution has been difficult, limiting integrative understanding of structure and function in complex biological tissues. We developed and applied a technology for 3D intact-tissue RNA sequencing, termed STARmap (spatially-resolved transcript amplicon readout mapping), which integrates hydrogel-tissue chemistry, targeted signal amplification, and in situ sequencing. The capabilities of STARmap were tested by mapping 160 to 1020 genes simultaneously in sections of mouse brain at single-cell resolution with high efficiency, accuracy, and reproducibility. Moving to thick tissue blocks, we observed a molecularly defined gradient distribution of excitatory-neuron subtypes across cubic millimeter–scale volumes (>30,000 cells) and a short-range 3D self-clustering in many inhibitory-neuron subtypes that could be identified and described with 3D STARmap.

Learning to See in the Dark

Abstract: Imaging in low light is challenging due to low photon count and low SNR. Short-exposure images suffer from noise, while long exposure can induce blur and is often impractical. A variety of denoising, deblurring, and enhancement techniques have been proposed, but their effectiveness is limited in extreme conditions, such as video-rate imaging at night. To support the development of learning-based pipelines for low-light image processing, we introduce a dataset of raw short-exposure low-light images, with corresponding long-exposure reference images. Using the presented dataset, we develop a pipeline for processing low-light images, based on end-to-end training of a fully-convolutional network. The network operates directly on raw sensor data and replaces much of the traditional image processing pipeline, which tends to perform poorly on such data. We report promising results on the new dataset, analyze factors that affect performance, and highlight opportunities for future work.

Engrams and circuits crucial for systems consolidation of a memory.

Abstract: Episodic memories initially require rapid synaptic plasticity within the hippocampus for their formation and are gradually consolidated in neocortical networks for permanent storage. However, the engrams and circuits that support neocortical memory consolidation have thus far been unknown. We found that neocortical prefrontal memory engram cells, which are critical for remote contextual fear memory, were rapidly generated during initial learning through inputs from both the hippocampal–entorhinal cortex network and the basolateral amygdala. After their generation, the prefrontal engram cells, with support from hippocampal memory engram cells, became functionally mature with time. Whereas hippocampal engram cells gradually became silent with time, engram cells in the basolateral amygdala, which were necessary for fear memory, were maintained. Our data provide new insights into the functional reorganization of engrams and circuits underlying systems consolidation of memory.

Learning to See in the Dark

Abstract: Imaging in low light is challenging due to low photon count and low SNR. Short-exposure images suffer from noise, while long exposure can induce blur and is often impractical. A variety of denoising, deblurring, and enhancement techniques have been proposed, but their effectiveness is limited in extreme conditions, such as video-rate imaging at night. To support the development of learning-based pipelines for low-light image processing, we introduce a dataset of raw short-exposure low-light images, with corresponding long-exposure reference images. Using the presented dataset, we develop a pipeline for processing low-light images, based on end-to-end training of a fully-convolutional network. The network operates directly on raw sensor data and replaces much of the traditional image processing pipeline, which tends to perform poorly on such data. We report promising results on the new dataset, analyze factors that affect performance, and highlight opportunities for future work. The results are shown in the supplementary video at this https URL