Allen Cell Imaging Collections

Tutorials

• Download and train label-free models by Greg Johnson
  
• Integrating single-cell sequencing and nuclear imaging data by Chengxiang Qiu and William Noble
  

Tools & Applications

• AICS Volume Viewer by Dan Toloudis
  
• AICSImageIO by Matthew Bowden, Jackson Brown, Jamie Sherman, Dan Toloudis
  
• Allen Cell Feature Explorer by Allen Institute for Cell Science
  
• Allen Cell Structure Segmenter by Jianxu Chen, Liya Ding, Matheus P. Viana, Melissa C. Hendershott, Ruian Yang, Irina A. Mueller, Susanne M. Rafelski
  
• Integrated Mitotic Stem Cell by Allen Institute for Cell Science
  
• Pytorch 3D Integrated Cell by Gregory R. Johnson, Rory M. Donovan-Maiye, Mary M. Maleckar
  
• Visual Guide to Human Cells by Allen Institute for Cell Science
  

Publications

• 4D hybrid model interrogates agent-level rules and parameters driving hiPS cell colony dynamics by Jessica S. Yu, Blair Lyons, Susanne Rafelski, Julie A. Theriot, Neda Bagheri & Graham T. Johnson
  
• A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes by Tanya Grancharova*, Kaytlyn A. Gerbin*, Alexander B. Rosenberg, Charles M. Roco, Joy E.Arakaki , Colette M. DeLizo, Stephanie Q. Dinh, Rory M. Donovan-Maiye, Matthew Hirano, Angelique M. Nelson, Joyce Tang, Julie A. Theriot, Calysta Yan, Vilas Menon, Sean P. Palecek, Georg Seelig & Ruwanthi N. Gunawardane
  
• A deep generative model of 3D single-cell organization by Rory M. Donovan-Maiye, Jackson M. Brown, Caleb K. Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A. Theriot, Mary M. Maleckar, Theo A. Knijnenburg & Gregory R. Johnson
  
• A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs) by Caroline Hookway*, Antoine Borensztejn*, Leigh K. Harris*, Sara Carlson, Gokhan Dalgin, Suraj Mishra, Nivedita Nivedita, Ellen M. Adams, Tiffany Barszczewski, Julie C. Dixon, Jacqueline H. Edmonds, Erik A. Ehlers, Alexandra J. Ferrante, Margaret A. Fuqua, Philip Garrison, Janani Gopalan, Benjamin W. Gregor, Maxwell J. Hedayati, Kyle N. Klein, Chantelle L. Leveille, Sean L. Meharry, Haley S. Morris, Gouthamrajan Nadarajan, Sandra A. Oluoch, Serge E. Parent, Amber Phan, Brock Roberts, Emmanuel E. Sanchez, M. Filip Sluzewski, Lev S. Snyder, Derek J. Thirstrup, John Paul Thottam, Julia R. Torvi, Gaea Turman, Matheus P. Viana, Lyndsay Wilhelm, Chamari S. Wijesooriya, Jie Yao, Julie A. Theriot, Susanne M. Rafelski & Ruwanthi N. Gunawardane
  
• Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy by Benjamin W. Gregor*, Mackenzie E. Coston*, Ellen M. Adams, Joy Arakaki, Antoine Borensztejn, Thao P. Do, Margaret A. Fuqua, Amanda Haupt, Melissa C. Hendershott, Winnie Leung, Irina A. Mueller, Aditya Nath, Angelique M. Nelson, Susanne M. Rafelski, Emmanuel E. Sanchez, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Winfried Wiegraebe, Brian P. Whitney, Calysta Yan, Ruwanthi N. Gunawardane & Nathalie Gaudreault
  
• Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes by Kaytlyn A. Gerbin*, Tanya Grancharova*, Rory M. Donovan-Maiye*, Melissa C. Hendershott*, Helen G. Anderson, Jackson M. Brown, Jianxu Chen, Stephanie Q. Dinh, Jamie L. Gehring, Gregory R. Johnson, HyeonWoo Lee, Aditya Nath, Angelique M. Nelson, M. Filip Sluzewski, Matheus P. Viana, Calysta Yan, Rebecca J. Zaunbrecher, Kimberly R. Cordes Metzler, Nathalie Gaudreault, Theo A. Knijnenburg, Susanne M. Rafelski, Julie A. Theriot & Ruwanthi N. Gunawardane
  
• Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories by Julie C. Dixon*, Christopher L. Frick*, Chantelle L. Leveille*, Philip Garrison, Peyton A. Lee, Saurabh S. Mogre, Benjamin Morris, Nivedita Nivedita, Ritvik Vasan, Jianxu Chen, Cameron L. Fraser, Clare R. Gamlin, Leigh K. Harris, Melissa C. Hendershott, Graham T. Johnson, Kyle N. Klein, Sandra A. Oluoch, Derek J. Thirstrup, M. Filip Sluzewski, Lyndsay Wilhelm, Ruian Yang, Daniel M. Toloudis, Matheus P. Viana, Julie A. Theriot & Susanne M. Rafelski
  
• Integrated intracellular organization and its variations in human iPS cells by Matheus P. Viana, Jianxu Chen*, Theo A. Knijnenburg*, Ritvik Vasan*, Calysta Yan*... Allen Institute for Cell Science... Graham T. Johnson, Ruwanthi N. Gunawardane, Nathalie Gaudreault, Julie A. Theriot & Susanne M. Rafelski
  
• Interpretable representation learning for 3D multi-piece intracellular structures using point clouds by Ritvik Vasan, Alexandra J. Ferrante, Antoine Borensztejn, Christopher L. Frick, Nathalie Gaudreault, Saurabh S. Mogre, Benjamin Morris, Guilherme G. Pires, Susanne M. Rafelski, Julie A. Theriot & Matheus P. Viana
  
• Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy by Chawin Ounkomol, Sharmishtaa Seshamani, Mary M. Maleckar, Forrest Collman & Gregory R. Johnson
  
• Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization by Brock Roberts*, Amanda Haupt*, Andrew Tucker, Tanya Grancharova, Joy Arakaki, Margaret A. Fuqua, Angelique Nelson, Caroline Hookway, Susan A. Ludmann, Irina A. Mueller, Ruian Yang, Rick Horwitz, Susanne M. Rafelski & Ruwanthi N. Gunawardane
  

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
  

Fly Brain Anatomy: FlyLight Gen1 and Split-GAL4 Imagery

Tutorials

• File Operations on AWS S3 by Rob Svirskas
  
• Scaling Neuroscience Research on AWS by Konrad Rokicki
  AWS LambdaAWS AppSyncAmazon DynamoDBAWS Step Functions
• Tutorial for neuronbridger (R API) by Alexander Bates
  
• Using Imagery on AWS S3 by Rob Svirskas
  

Tools & Applications

• Color Depth Search Fiji Plugin by Hideo Otsuna
  
• Fly Light Split-GAL4 Driver Collection by Rob Svirskas
  
• FlyLight Project Website by Geoffrey Meissner
  
• NeuronBridge by Jody Clements, Rob Svirskas, Hideo Otsuna, Cristian Goina, Konrad Rokicki
  

Publications

• A GAL4-Driver Line Resource for Drosophila Neurobiology by Arnim Jenett, Gerald M Rubin, Teri-TB Ngo, David Shepherd, Christine Murphy, Heather Dionne, Barret D Pfeiffer, Amanda Cavallaro, Donald Hall, Jennifer Jeter, Nirmala Iyer, Dona Fetter, Joanna H Hausenfluck, Hanchuan Peng, Eric T Trautman, Robert R Svirskas, Eugene W Myers, Zbigniew R Iwinski, Yoshinori Aso, Gina M DePasquale, Adrianne Enos, Phuson Hulamm, Shing Chun Benny Lam, Hsing-Hsi Li, Todd R Laverty, Fuhui Long, Lei Qu, Sean D Murphy, Konrad Rokicki, Todd Safford, Kshiti Shaw, Julie H Simpson, Allison Sowell, Susana Tae, Yang Yu, Christopher T Zugates
  
• An image resource of subdivided Drosophila GAL4-driver expression patterns for neuron-level searches by Geoffrey W Meissner, Zachary Dorman, Aljoscha Nern, Kaitlyn Forster, Theresa Gibney, Jennifer Jeter, Lauren Johnson, Yisheng He, Kelley Lee, Brian Melton, Brianna Yarbrough, Jody Clements, Cristian Goina, Hideo Otsuna, Konrad Rokicki, Robert R Svirskas, Yoshinori Aso, Gwyneth M Card, Barry J Dickson, Erica Ehrhardt, Jens Goldammer, Masayoshi Ito, Wyatt Korff, Ryo Minegishi, Shigehiro Namiki, Gerald M Rubin, Gabriella Sterne, Tanya Wolff, Oz Malkesman, FlyLight Project Team
  
• An unbiased template of the Drosophila brain and ventral nerve cord by John A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, Jennifer Jeter, Geoffrey Meissner, Aljoscha Nern, Jennifer Colonell, Oz Malkesman, Kei Ito, Stephan Saalfeld
  
• Color depth MIP mask search: a new tool to expedite Split-GAL4 creation by Hideo Otsuna, Masayoshi Ito, Takashi Kawase
  
• The neuronal architecture of the mushroom body provides a logic for associative learning by Yoshinori Aso, Daisuke Hattori, Yang Yu, Rebecca M Johnston, Nirmala A Iyer, Teri-TB Ngo, Heather Dionne, LF Abbott, Richard Axel, Hiromu Tanimoto, Gerald M Rubin
  

Low Altitude Disaster Imagery (LADI) Dataset

Tutorials

• LADI v1 Tutorials by Andrew Weinert, Jianyu Mao, Kiana Harris, Nae-Rong Chang, Caleb Pennell, Yiming Ren, Ryan Earley, Nadia Dimitrova
  
• LADI v2 Overview by Jeffrey Liu, Sam Scheele, Katherine Picchione
  

Tools & Applications

• NIST TRECVID 2020 - Disaster Scene Description and Indexing (DSDI) by TREC Video Retrieval Evaluation (TRECVID)
  
• Remote Sensing for Disaster Response Course by Beaver Works Summer Institute
  

Publications

• Accelerate disaster response with computer vision for satellite imagery using Amazon SageMaker and Amazon Augmented AI by Vamshi Krishna Enabothala, Morgan Dutton, and Sandeep Verma
  
• An overview on the evaluated video retrieval tasks at TRECVID 2022 by George Awad, Keith Curtis, Asad Butt, Jonathan Fiscus, Afzal Godil, Yooyoung Lee, Andrew Delgado, Eliot Godard, Lukas Diduch, Jeffrey Liu, Yvette Graham, Georges Quenot
  
• Evaluating Multiple Video Understanding and Retrieval Tasks at TRECVID 2021 by George Awad, Asad Butt, Keith Curtis, Jonathan G. Fiscus, Afzal A. Godil, Yooyoung Lee, Andrew Delgado, Eliot Godard, Baptiste Chocot, Lukas Diduch, Jeffrey Liu, Yvette Graham, Gareth Jones, Georges Quenot
  
• Large Scale Organization and Inference of an Imagery Dataset for Public Safety by Jeffrey Liu, David Strohschein, Siddharth Samsi, Andrew Weinert
  
• Train and Deploy an Image Classifier for Disaster Response by Jianyu Mao, Kiana Harris, Nae-Rong Chang, Caleb Pennell, Yiming Ren
  
• TRECVID 2020: A comprehensive campaign for evaluating video retrieval tasks across multiple application domains by George Awad, Asad A. Butt, Keith Curtis, Jonathan Fiscus, Afzal Godil, Yooyoung Lee, Andrew Delgado, Jesse Zhang, Eliot Godard, Baptiste Chocot, Lukas Diduch, Jeffrey Liu, Alan F. Smeaton, Yvette Graham, Gareth J. F. Jones, Wessel Kraaij, Georges Quenot
  
• Video Testing at the FirstNet Innovation and Test Lab Using a Public Safety Dataset by Chris Budny, Jeffrey Liu, Andrew Weinert
  

Open NeuroData

Tutorials

• Download by Benjamin Falk
  
• Visualization using Neuroglancer by Benjamin Falk
  

Tools & Applications

• CloudVolume by William Silversmith
  
• Igneous by William Silversmith
  
• Neuroglancer by Jeremy Maitin-Shepard
  

Publications

• A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data by J. T. Vogelstein, E. Perlman, B. Falk, A. Baden, W. Gray Roncal, V. Chandrashekhar, F. Collman, S. Seshamani, J. L. Patsolic, K. Lillaney, M. Kazhdan, R. Hider, D. Pryor, J. Matelsky, T. Gion, P. Manavalan, B. Wester, M. Chevillet, E. T. Trautman, K. Khairy, E. Bridgeford, D. M. Kleissas, D. J. Tward, A. K. Crow, B. Hsueh, M. A. Wright, M. I. Miller, S. J. Smith, R. J. Vogelstein, K. Deisseroth, and R. Burns
  
• From cosmos to connectomes: The evolution of data-intensive science by R. Burns, J. T. Vogelstein, and A. S. Szalay
  
• The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience by R. Burns, W. G. Roncal, D. Kleissas, K. Lillaney, P. Manavalan, E. Perlman, D. R. Berger, D. D. Bock, K. Chung, L. Grosenick, N. Kasthuri, N. C. Weiler, K. Deisseroth, M. Kazhdan, J. Lichtman, R. C. Reid, S. J. Smith, A. S. Szalay, J. T. Vogelstein, and R. J. Vogelstein.
  
• To the Cloud! A Grassroots Proposal to Accelerate Brain Science Discovery by J. T. Vogelstein, B. Mensh, M. Häusser, N. Spruston, A. C. Evans, K. Kording, K. Amunts, C. Ebell, J. Muller, M. Telefont, S. Hill, S. P. Koushika, C. Calì, P. A. Valdés-Sosa, P. B. Littlewood, C. Koch, S. Saalfeld, A. Kepecs, H. Peng, Y. O. Halchenko, G. Kiar, M. M. Poo, J. B. Poline, M. P. Milham, A. P. Schaffer, R. Gidron, H. Okano, V. D. Calhoun, M. Chun, D. M. Kleissas, R. J. Vogelstein, E. Perlman, R. Burns, R. Huganir, and M. I. Miller
  

Earth Observation Data Cubes for Brazil

Tutorials

• Tile Map Service to view Image Collections from Brazil Data Cube Catalog by Brazil Data Cube
  
• Using Python to Access Image Collections Data (Jupyter notebook) by Brazil Data Cube
  

Tools & Applications

• cube-builder-aws - Application to generate data cubes on AWS environment. by Brazil Data Cube
  
• rstac - R library to query and download Image Collections from Brazil Data Cube Catalog on Amazon S3 by Brazil Data Cube
  

Publications

• Building Earth Observation Data Cubes on AWS by Ferreira, K R; Queiroz, G R; Marujo, R F B; Costa, R W. 
  
• Earth Observation Data Cubes for Brazil: Requirements, Methodology and Products. by K. R. Ferreira, et al.
  
• Using Remote Sensing Images and Cloud Services on AWS to Improve Land Use and Cover Monitoring by K. R. Ferreira, et al.
  

Capella Space Synthetic Aperture Radar (SAR) Open Dataset

Tutorials

• Scaling GEO Images in QGIS by Capella Space
  

Tools & Applications

• Python SDK for api.capellaspace.com by Capella Space
  
• Single Look Complex data reader for Capella SLC images - python module to convert Capella SLC data into an amplitude image. by Capella Space
  

Publications

• Analyzing LiDAR and SAR data with Capella Space and TileDB by Stavros Papadopoulos
  
• Open SAR data and scalable analytics by Norman Barker
  
• Radar Generalized Image Quality Equation Applied to Capella Open Dataset by Wade Schwartzkopf, Jason Brown, Gordon Farquharson, Craig Stringham, Michael Duersch, Jordan Heemskerk
  

NYU Langone & FAIR FastMRI Dataset

Tutorials

• FastMRI Tutorial (Jupyter Notebook) by Tullie Murrell
  
• How to Get Started Working with the FastMRI Dataset (and why you should!) by Kevin Hodges
  

Publications

• Advancing machine learning for MR image reconstruction with an open competition:Overview of the 2019 fastMRI challenge by Knoll et al (2020)
  
• Assessment of the generalization of learned image reconstruction and the potential for transfer learning. by Knoll et al (2019)
  
• Deep Learning Methods for Parallel Magnetic Resonance Image Reconstruction by Knoll et al (2019)
  
• fastMRI:An Open Dataset and Benchmarks for Accelerated MRI by Zbontar et al (2019)
  

PoroTomo

Tutorials

• PoroTomo DAS Data Processing Tutorial for hdf5 Files by Nicole Taverna and Michael Rossol
  
• PoroTomo DAS Data Processing Tutorial for hdf5 Files via HSDS and h5pyd by Michael Rossol and Nicole Taverna
  
• PoroTomo DAS Data Processing Tutorial for SEG-Y Files by Nicole Taverna and Ross Ring-Jarvi
  

Publications

• DAS and DTS at Brady Hot Springs: Observations about Coupling and Coupled Interpretations by Douglas E. Miller, Thomas Coleman, Xiangfang Zeng, Jeremy R. Patterson , Elena C. Reinnisch, Michael A. Cardiff, Herbert F. Wang, Dante Fratta, Whitney Trainor-Guitton, Clifford H. Thurber, Michelle ROBERTSON, Kurt FEIGL, and The PoroTomo Team
  
• Ground motion response to an ML 4.3 earthquake using co-located distributed acoustic sensing and seismometer arrays by Herbert F Wang, Xiangfang Zeng, Douglas E Miller, Dante Fratta, Kurt L Feigl, Clifford H Thurber, Robert J Mellors
  
• PoroTomo Final Technical Report: Poroelastic Tomography by Adjoint Inverse Modeling of Data from Seismology, Geodesy, and Hydrology by Kurt L. Feigl, Lesley M. Parker, and the PoroTomo Team
  

RACECAR Dataset

Tutorials

• RACECAR Tutorials - nuScenes by John Chrosniak
  
  
• RACECAR Tutorials - ROS2 Localization by Amar Kulkarni
  
• RACECAR Tutorials - ROS2 Visualization by Amar Kulkarni, Utkarsh Chirimar
  

Tools & Applications

• rosbag2nuscenes conversion library by John Chrosniak, Emory Ducote, John Link, Madhur Behl
  

Publications

• RACECAR--The Dataset for High-Speed Autonomous Racing by Amar Kulkarni, John Chrosniak, Emory Ducote, Florian Sauerbeck, Andrew Saba, Utkarsh Chirimar, John Link, Marcello Cellina, and Madhur Behl
  

High Resolution Canopy Height Maps by WRI and Meta

Tools & Applications

• Global Canopy Height on Earth Engine by Meta and WRI
  

Publications

• Every tree counts: Large-scale mapping of canopy height at the resolution of individual trees by Jamie Tolan, Camille Couprie, and Tracy Johns
  
• Sub-meter resolution canopy height maps using self-supervised learning and a vision transformer trained on Aerial and GEDI Lidar by Jamie Tolan, Hung-I Yang, Ben Nosarzewski, Guillaume Couairon, Huy Vo, John Brandt, Justine Spore, Sayantan Majumdar, Daniel Haziza, Janaki Vamaraju, Theo Moutakanni, Piotr Bojanowski, Tracy Johns, Brian White, Tobias Tiecke, Camille Couprie
  
• Using Artificial Intelligence to Map the Earth’s Forests by Jamie Tolan, Camille Couprie, John Brandt, Justine Spore, Tobias Tiecke, Tracy Johns and Patrick Nease
  

Mouse Brain Anatomy: MouseLight Imagery

Tools & Applications

• HortaCloud by David Schauder, Donald J. Olbris, Jody Clements, Cristian Goina, Robert R. Svirskas, Konrad Rokicki
  
• MouseLight NeuronBrowser by Tiago A. Ferreira, Jayaram Chandrashekar
  
• MouseLight Project Website by Tiago A. Ferreira, Jayaram Chandrashekar
  

Publications

• Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain by Johan Winnubst, Erhan Bas, Tiago A. Ferreira, Zhuhao Wu, Michael N. Economo, Patrick Edson, Ben J. Arthur, Christopher Bruns, Konrad Rokicki, David Schauder, Donald J. Olbris, Sean D. Murphy, David G. Ackerman, Cameron Arshadi, Perry Baldwin, Regina Blake, Ahmad Elsayed, Mashtura Hasan, Daniel Ramirez, Bruno Dos Santos, Monet Weldon, Amina Zafar, Joshua T. Dudman, Charles R. Gerfen, Adam W. Hantman, Wyatt Korff, Scott M. Sternson, Nelson Spruston, Karel Svoboda, Jayaram Chandrashekar
  

SiPeCaM (Sitios Permanentes de la Calibración y Monitoreo de la Biodiversidad)

Tutorials

• Sample search query on all images files for cumulus 92, using Alfresco. by Carolina Acosta
  Amazon S3
• Sample search query on november audio files for cumulus 92, using Alfresco. by Carolina Acosta
  Amazon S3
• Sample search query on november video files for cumulus 92, using Alfresco. by Carolina Acosta
  Amazon S3

Publications

• Sitios Permanente de la Calibración y Monitoreo de la Biodiversidad by Michael Schmidt et. al.
  

Allen Ivy Glioblastoma Atlas

Tutorials

• Accessing Ivy Glioblastoma Atlas Project data by Allen Institute for Brain Science
  

Tools & Applications

• Ivy Glioblastoma Atlas Project by Allen Institute for Brain Science
  

Publications

• An anatomic transcriptional atlas of human glioblastoma by Ralph Puchalski, et al.
  

Allen Mouse Brain Atlas

Tutorials

• Accessing Allen Mouse Brain Atlas data by Allen Institute for Brain Science
  

Tools & Applications

• Allen Mouse Brain Atlas by Allen Institute for Brain Science
  

Publications

• Genome-wide atlas of gene expression in the adult mouse brain by Ed Lein, et al.
  

NIFS Large Helical Device (LHD) Experiment

Tutorials

• Data handling in the LHD experiments -- Guide for the collaborator (pdf) by Satoshi Ohdachi
  

Tools & Applications

• How to retrieve diagnostic raw data and/or primarily processed data using "Retrieve" by NIFS LABCOM
  

Publications

• Data Acquisition and Management System of LHD by Hideya Nakanishi, et al.
  

National Cancer Institute Imaging Data Commons (IDC) Collections

Tutorials

• IDC "Getting started" tutorial series by Imaging Data Commons team
  

Tools & Applications

• IDC Portal by Imaging Data Commons team
  

Publications

• NCI Imaging Data Commons by Fedorov A, Longabaugh W, Pot D, Clunie D, Pieper S, Aerts H, et al.
  

PD12M

Tutorials

• Downloading Images by Spawning
  
• Working with the Metadata by Spawning
  

Tools & Applications

• Hugging Face Dataset by Spawning
  
• Source.Plus by Spawning
  

Publications

• Datasheet by Spawning
  
• PD12M: A Large-Scale Image Captioning Dataset by Jordan Meyer, Nick Padgett, Laura Exline, Cullen Miller
  

Aurora Multi-Sensor Dataset

Tutorials

• Introduction to Visualizing Sensor Types (Jupyter notebook) by Andrei Bârsan (note: Aurora makes no representations as to the accuracy or functionality of the tutorial)
  Amazon SageMaker Studio Lab

Publications

• "Pit30M: A benchmark for global localization in the age of self-driving cars", in 2020 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS) (pp. 4477-4484) by Martinez, J., Doubov, S., Fan, J., Bârsan, I. A., Wang, S., Máttyus, G., Urtasun, R.
  

DigitalCorpora

Publications

• Bringing Science to Digital Forensics with Standardized Forensic Corpora by Garfinkel, Farrell, Roussev and Dinolt
  
• Creating Realistic Corpora for Forensic and Security Education by Woods, K., Christopher Lee, Simson Garfinkel, David Dittrich, Adam Russel, Kris Kearton
  

Satellogic EarthView dataset

Tutorials

• Explore Satellogic EarthView in SageMaker Studio Lab (SMSL) by Javier Marin
  
  Amazon SageMaker Studio Lab

Publications

• EarthView: A Large Scale Remote Sensing Dataset for Self-Supervision by Velázquez, Diego and Rodríguez, Pau and Alonso, Sergio and Gonfaus, Josep M. and González, Jordi and, Richarte, Gerardo and Marín, Javier and Bengio, Yoshua and Lacoste, Alexandre
  

Sub-Meter Canopy Tree Height of California in 2020 by CTrees.org

Publications

• Canopy Height Unlocked: California Forest Resources Detailed in New Tree-level Map by Daniel Melling
  
• Sub-Meter Tree Height Mapping of California using Aerial Images and LiDAR-Informed U-Net Model by Fabien H Wagner, Sophia Roberts, Alison L Ritz, Griffin Carter, Ricardo Dalagnol, Samuel Favrichon, Mayumi CM Hirye, Martin Brandt, Philippe Ciais and Sassan Saatchi
  

Allen Brain Observatory - Visual Coding AWS Public Data Set

Tutorials

• Use the Allen Brain Observatory – Visual Coding on AWS by Nika Keller, David Feng
  

Allen Institute for Neural Dynamics - Mouse Neuroanatomy and Physiology Data

Tutorials

• AIND Open Data Access by David Feng, Saskia de Vries
  

High Resolution Population Density Maps + Demographic Estimates by CIESIN and Meta

Tutorials

• Investigating environmental characteristics of US cities using publicly available ASDI datasets by Darren Ko
  
  Amazon SageMaker Studio Lab

NYUMets Brain Dataset

Publications

• Longitudinal deep neural networks for assessing metastatic brain cancer on a massive open benchmark. by Link et al (2023)
  

Ohio State Cardiac MRI Raw Data (OCMR)

Tutorials

• OCMR Tutorial by Chong Chen
  

Xiph.Org Test Media

Tutorials

• Encoding video with AV1 on EC2 by Thomas Daede