Cell Painting Gallery

Tutorials

• Cell Painting wiki by Multiple Authors
  
• Center for Open Bioimage Analysis (COBA) YouTube Channel - video tutorials of CellProfiler and other softwares by Multiple Authors
  
• Image-based Profiling Handbook - for processing image-based profiling datasets using CellProfiler and pycytominer by Multiple Authors
  
• Image-based profiling introductory exercise - data and an exercise on exploring image-based profiles, including understanding the various data levels by Beth Cimini
  
• Scientific Community Image Forum - for software-oriented aspects of scientific imaging including analysis, processing, and acquisition by Multiple Authors
  

Tools & Applications

• Accelerating Drug Discovery with high-throughput Cell Painting on AWS by Chris Kaspar
  
• Deep Profiler - Morphological profiling using deep learning by Multiple Authors
  
• Distributed CellProfiler - Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure by Multiple Authors
  
• Image-based Profiling Recipe by Multiple Authors
  
• Pycytominer - Data processing functions for profiling perturbations by Multiple Authors
  

Publications

• A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay by Bray M-A, Gustafsdottir SM, Rohban MH, Singh S, Ljosa V, Sokolnicki KL, Bittker JA, Bodycombe NE, Dancik V, Hasaka TP, Hon CS, Kemp MM, Li K, Walpita D, Wawer MJ, Golub TR, Schreiber SL, Clemons PA, Shamji AF, & Carpenter AE
  
• Cell Painting predicts impact of lung cancer variants by Caicedo JC, Arevalo J, Piccioni F, Bray MA, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, & Singh S
  
• Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes by Bray M-A, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, & Carpenter AE
  
• Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects by Singh S, Wu X, Ljosa V, Bray M-A, Piccioni F, Root DE, Doench JG, Boehm JS, & Carpenter AE
  
• Multiplex Cytological Profiling Assay to Measure Diverse Cellular States by Gustafsdottir SM, Ljosa V, Sokolnicki KL, Wilson JA, Walpita D, Kemp MM, Seiler KP, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, and Shamji AF
  
• Systematic morphological profiling of human gene and allele function via Cell Painting by Rohban MH, Singh S, Wu X, Berthet JB, Bray M-A, Shrestha Y, Varelas X, Boehm JS, & Carpenter AE
  
• Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling by Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, BodycombeNE, Marton MA, Sokolnicki KL, Bray M-A, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CSK, Duvall JR, Wilson JA, Bittker JA, Dancik V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, & Clemons PA
  

Japanese Tokenizer Dictionaries

Tutorials

• Fugashi Word Count Tutorial by Paul O'Leary McCann
  Amazon SageMaker

Tools & Applications

• unidic-py by Paul O'Leary McCann
  

Publications

• How to Tokenize Japanese in Python by Paul O'Leary McCann
  

Emory Knee Radiograph (MRKR) dataset

Tutorials

• Example Notebook by Emory-HITI
  

Publications

• Emory Knee Radiograph Dataset by Brandon Price, Jason Adleberg, Kaesha Thomas, Zach Zaiman, Aawez Mansuri, Beatrice Brown-Mulry, Chima Okecheukwu, Judy Gichoya, Hari Trivedi.
  

NIH NCBI PubMed Central (PMC) Article Datasets - Full-Text Biomedical and Life Sciences Journal Articles on AWS

Tutorials

• Accessing PMC Article Datasets Using Amazon Web Services by NCBI PMC
  

Tools & Applications

• Extracting insights from PubMed articles using Amazon Q Business by Bharath Gunapati and Stefan Mationg
  

AI2 Meaningful Citations Data Set

Publications

• Identifying Meaningful Citations by Marco Valenzuela, Vu A. Ha, Oren Etzioni
  

AI2 Reasoning Challenge (ARC) 2018

Publications

• Think you have Solved Question Answering? Try ARC, the AI2 Reasoning Challengg by Peter Clark, Isaac Cowhey, Oren Etzioni, Tushar Khot, Ashish Sabharwal, Carissa Schoenick, Oyvind Tafjord
  

Legal Entity Identifier (LEI) and Legal Entity Reference Data (LE-RD)

Publications

• AWS hosts new open dataset to help businesses identify climate finance risks and investments by AWS Public Sector Blog Team
  

RSNA Abdominal Trauma Detection (RSNA-ABT)

Publications

• The RSNA Abdominal Traumatic Injury CT (RATIC) Dataset by Rudie, Jeffrey D.
  

RSNA Cervical Spine Fracture Detection (RSNA-CSF) Dataset

Publications

• The RSNA Cervical Spine Fracture CT Dataset by Ming, Hui Lin
  

RSNA Intracranial Hemorrhage Detection

Publications

• Construction of a Machine Learning Dataset through Collaboration: The RSNA 2019 Brain CT Hemorrhage Challenge by Rudie, Jeffrey D.
  

RSNA Pulmonary Embolism Detection

Publications

• The RSNA Pulmonary Embolism CT Dataset by Colak, Errol
  

Synthea Coherent Data Set

Publications

• The “Coherent Data Set”: Combining Patient Data and Imaging in a Comprehensive Synthetic Health Record. by Walonoski J, Hall D, Bates KM, Farris MH, Dagher J, Downs ME, Sivek RT, Wellner B, Gregorowicz A, Hadley M, Campion FX, Levine L, Wacome K, Emmer G, Kemmer A, Malik M, Hughes J, Granger E, Russell S.
  

recount3

Tutorials

• recount3 quick start guide by Leonardo Collado-Torres