A5073908382- Cell Image Analysis Techniques
- Single-cell and spatial transcriptomics
- Advanced Electron Microscopy Techniques and Applications
- Parasites and Host Interactions
- Advanced Memory and Neural Computing
- Advanced Fluorescence Microscopy Techniques
- 3D Printing in Biomedical Research
- Advanced Neuroimaging Techniques and Applications
- Cancer, Hypoxia, and Metabolism
- Neural dynamics and brain function
- Genetics, Aging, and Longevity in Model Organisms
- Electron and X-Ray Spectroscopy Techniques
- Machine Learning in Materials Science
- Computational Drug Discovery Methods
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- Functional Brain Connectivity Studies
- Machine Learning and Algorithms
- Research Data Management Practices
- Spaceflight effects on biology
- Cervical Cancer and HPV Research
- Vitamin D Research Studies
- AI in cancer detection
- Renal cell carcinoma treatment
- Genomics and Phylogenetic Studies
Massachusetts Institute of Technology
2012-2025
IIT@MIT
2020
Harvard University
2017-2019
Broad Institute
2011-2018
University of Wisconsin–Madison
2011
CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe 3.0, a new version of software supporting both whole-volume and plane-wise three-dimensional (3D) stacks, increasingly common biomedical research. CellProfiler's infrastructure is greatly improved, provide protocol for cloud-based, large-scale processing. New plugins enable running pretrained deep learning models on images. Designed by...
Abstract Summary: There is a strong and growing need in the biology research community for accurate, automated image analysis. Here, we describe CellProfiler 2.0, which has been engineered to meet needs of its user base. It more robust friendly, with new algorithms features facilitate high-throughput work. ImageJ plugins can now be run within pipeline. Availability Implementation: 2.0 free open source, available at http://www.cellprofiler.org under GPL v. 2 license. as packaged application...
To stimulate progress in automating the reconstruction of neural circuits, we organized first international challenge on 2D segmentation electron microscopic (EM) images brain. Participants submitted boundary maps predicted for a test set images, and were scored based their agreement with consensus human expert annotations. The winning team had no prior experience EM employed convolutional network. This "deep learning" approach has since become accepted as standard images. continued to...
Abstract Neuronal ensembles that hold specific memory (memory engrams) have been identified in the hippocampus, amygdala, or cortex. However, it has hypothesized engrams of a are distributed among multiple brain regions functionally connected, referred to as unified engram complex. Here, we report partial map complex for contextual fear conditioning by characterizing encoding activated neuronal 247 using tissue phenotyping mice. The mapping was aided an index, which 117 cFos + holding with...
Abstract We describe a computer‐controlled 10 μm spot size laser scanning cytometer for making multiple wavelength fluorescence and scatter measurements of unconstrained cells on surface such as microscope slide. Designated areas slides placed stage are automatically scanned, which generate above‐threshold or values found individually processed to determine list measurement parameters. For each parameter, this contains the integrated peak bit pattern images scan window centered cell. The...
Imaging flow cytometry (IFC) enables the high throughput collection of morphological and spatial information from hundreds thousands single cells. This content, rich image data can in theory resolve important biological differences among complex, often heterogeneous samples. However, analysis is performed a highly manual subjective manner using very limited techniques combination with conventional gating strategies. approach not scalable to available image-based features per cell thus makes...
ABSTRACT Studying the function and dysfunction of complex biological systems necessitates comprehensive understanding individual cells. Advancements in three-dimensional (3D) tissue processing imaging modalities have enabled rapid visualization phenotyping cells their spatial context. However, system-wide interrogation within large intact remains challenging, low throughput, error-prone owing to lack robust labeling technologies. Here we introduce a rapid, versatile, scalable method, eFLASH,...
Understanding cellular architectures and their connectivity is essential for interrogating system function dysfunction. However, we lack technologies mapping the multiscale details of individual cells in human organ-scale system. We developed a platform that simultaneously extracts spatial, molecular, morphological, information from same brain. The includes three core elements: vibrating microtome ultraprecision slicing large-scale tissues without losing (MEGAtome), polymer hydrogel-based...
Schistosomiasis is a debilitating neglected tropical disease, caused by flatworms of Schistosoma genus. The treatment relies on single drug, praziquantel (PZQ), making the discovery new compounds extremely urgent. In this work, we integrated QSAR-based virtual screening (VS) mansoni thioredoxin glutathione reductase (SmTGR) inhibitors and high content (HCS) aiming to discover antischistosomal agents. Initially, binary QSAR models for inhibition SmTGR were developed validated using...
Schistosomiasis is a neglected tropical disease that affects millions of people worldwide. Thioredoxin glutathione reductase Schistosoma mansoni (SmTGR) validated drug target plays crucial role in the redox homeostasis parasite. We report discovery new chemical scaffolds against S. using combi-QSAR approach followed by virtual screening commercial database and confirmation top ranking compounds vitro experimental evaluation with automated imaging schistosomula adult worms. constructed 2D 3D...
Patients with a germline mutation in von Hippel-Lindau (VHL) develop renal cell cancers and hypervascular tumors of the brain, adrenal glands, pancreas as well erythrocytosis. These phenotypes are driven by aberrant expression HIF2α, which induces genes involved proliferation, angiogenesis, red blood production. Currently, there no effective treatments available for VHL disease. Here, using an animal model VHL, we report marked improvement VHL-associated following treatment HIF2α inhibitors....
The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data metadata in reusable way. First developed magnetic resonance imaging (MRI) datasets, the community-led evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, quantitative MRI (qMRI). In this work, we present an extension BIDS microscopy data, along with example datasets. Microscopy-BIDS supports common methods, including 2D/3D,
Connectomics has recently begun to image brain tissue at nanometer resolution, which produces petabytes of data. This data must be aligned, labeled, proofread, and formed into graphs, each step this process requires visualization for human verification. As such, we present the BUTTERFLY middleware, a scalable platform that can handle massive interactive in connectomics. Our outputs geometry suitable hardware-accelerated rendering, abstracts low-level wrangling enable faster development new...
Multiparameter laser scanning cytometry has been applied to the automatic counting of probe spots and simultaneous measurement cellular DNA for fluorescence in situ hybridization (FISH) prepared specimens counterstained with propidium iodide. Relatively low resolution imaging, highly variable fluorescence, spectral overlap counterstain autofluorescence required development an image processing method detect isolate FISH spots. Inability properly apportion detected because overlapping spot...
Abstract Here we describe an image processing pipeline for quantitative analysis of terabyte-scale volumetric images SHIELD-processed mouse brains imaged with light-sheet microscopy. The utilizes open-source packages destriping, stitching, and atlas alignment that are optimized parallel processing. destriping step removes stripe artifacts, corrects uneven illumination, offers over 100x speed improvements compared to previously reported algorithms. stitching module builds upon Terastitcher...
Paroxetine is a new anti-schistosomal lead with potent activity against schistosomula and adult life stages of <italic>S. mansoni.</italic>
Abstract Understanding cellular architectures and their connectivity is essential for interrogating system function dysfunction. However, we lack technologies mapping the multi-scale details of individual cells in human organ-scale system. To address this challenge, developed a platform that simultaneously extracts spatial, molecular, morphological, information from same brain, by integrating novel chemical, mechanical, computational tools. The includes three key tools: (i) vibrating...