Imageomics | Baserow

Publication Title

Biodiversity Image Quality Metadata Augments Convolutional Neural Network Classification of Fish Species

Automatic Metadata Generation for Fish Specimen Image Collections

Hierarchy-guided neural network for species classification

Perspectives in machine learning for wildlife conservation

Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish

Learning to Detect Mobile Objects from LiDAR Scans Without Labels

One Step at a Time: Long-Horizon Vision-and-Language Navigation with Milestones

A process for generating new cross-disciplinary projects

Learning with Free Object Segments for Long-Tailed Instance Segmentation

Toward a flexible metadata pipeline for fish specimen images

Automated landmarking via multiple templates

The impacts of fine-tuning, phylogenetic distance, and sample size on big-data bioacoustics

Deep learning enabled multi-organ segmentation of mouse embryos

An effective way to organize research coordination meetings

Imageomics Approach to Understanding Visual Biological Trait Similarities using Butterfly Mimicry as a Model System

Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks

Machine learning reveals relationships between song, climate, and migration in coastal Zonotrichia leucophrys

An Open-Source Photogrammetry Workflow for Reconstructing 3D Models

Complexity leadership in action: a team science case study

On image quality metadata, fair in ML, AI-readiness and reproductibility: Fish-air example

How to organize an "all-hands" meeting

Holistic Transfer: Towards Non-Disruptive Fine-Tuning with Partial Target Data

A Framework for Autonomic Computing for In Situ Imageomics

KABR: In-Situ Dataset for Kenyan Animal Behavior Recognition from Drone Videos

Bats of a feather: Range characteristics and wing morphology predict phylogeographic breaks in volant vertebrates

A FAIR and modular image-based workflow for knowledge discovery in the emerging field of imageomics

Species-Agnostic Patterned Animal Re-identification by Aggregating Deep Local Features

BaboonLand Dataset: Tracking Primates in the Wild and Automating Behaviour Recognition from Drone Videos

Leveraging Descriptor Learning and Functional Map-based Shape Matching for Automatic Landmark Acquisition

A Simple Interpretable Transformer for Fine-Grained Image Classification and Analysis

Integrating Biological Data into Autonomous Remote Sensing Systems for In Situ Imageomics: A Case Study for Kenyan Animal Behavior Sensing with Unmanned Aerial Vehicles (UAVs)

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DOI/Link

Author(s)

Insitute

Publication Date

Code

Supplementary Materials (Data, Notebooks, Models)

Keywords

https://doi.org/10.1007/978-3-030-71903-6_1

Jeremy Leipzig, Yasin Bakis, Xiaojun Wang, Mohannad Elhamod, Kelly Diamond, Wasila Dahdul, Anuj Karpatne, Murat Maga, Paula Mabee, Henry Bart, Jane Greenberg

Imageomics

https://github.com/hdr-bgnn/iqm

https://github.com/SlicerMorph/Mouse_Models/tree/main/Models

Image classification, Convolutional neural networks, Image metadata, Quality metadata, Imageomics

https://ieeexplore.ieee.org/document/9651834

Joel Pepper, Jane Greenberg, Yasin Bakis, Xiaojun Wang, Henry Bart, David Breen

Imageomics

Bioinformatics, Metadata, Image analysis, Applied Machine Learning, Imageomics

https://doi.org/10.1111/2041-210X.13768

Mohannad Elhamod, Kelly Diamond, Murat Maga, Yasin Bakis, Henry Bart, Paula Mabee, Wasila Dahdul, Jeremy Leipzig, Jane Greenberg, Brian Avants, Anuj Karpatne

Imageomics

Imageomics, Machine Learning, Neural Networks, science guided Machine Learning, species classification, Taxonomy

https://www.nature.com/articles/s41467-022-27980-y

Devis Tuia, Benjamin Kellenberger, Sara Beery, Blair Costelloe, Silvia Zuffi, Benjamin Risse, Alexander Mathis, Mackenzie Mathis, Frank van Langevelde, Tilo Burghardt, Roland Kays, Holger Klinck, Martin Wikelski, Iain Couzin, Grant van Horn, Margaret Crofoot, Charles Stewart, Tanya Berger-Wolf

Imageomics

Imageomics, Computer Vision, Animal biometrics, Conservation, Machine Learning, Remote Sensing, Artificial Intelligence

https://doi.org/10.1242/bio.058948

Kelly Diamond, Sara Rolfe, Ronald Kwon, Murat Maga

Imageomics

https://github.com/SlicerMorph/ZF_Skull_atlas/

Imageomics, Csv-to-json, Slicer, Slicermorph, Cranial morphology, Osteogenesis imperfecta, Geometric morphometrics, Computational anatomy

https://doi.org/10.48550/arXiv.2203.15882

Yurong You, Katie Luo, Cheng Perng Phoo, Wei-Lun Chao, Wen Sun, Bharath Hariharan, Mark Campbell, Kilian Weinberger

Imageomics

https://github.com/YurongYou/MODEST

https://github.com/open-mmlab/OpenPCDet/tree/master/tools/cfgs/kitti_models

Imageomics, Recognition, Detection, Categorization, Retrieval, 3D from multi-view and sensors, Navigation and Autonomous driving, Transfer/low-shot/long-tail learning, Training, Three-dimensional displays, Laser radar, Navigation, Detectors, Pattern recognition, Sensors, LiDAR Scans, Mobile Objects, Detection Accuracy, Object Detection, Unlabeled Data, Simple Heuristics, 3D Object Detection, Neural Network, Training Set, Training Data, Pedestrian, Intersection Over Union, Point Cloud, Bounding Box, Objective Data, Autonomous Vehicles, Object Location, Ground Truth Labels, Object Shape, High Recall, Noisy Labels, Background Points, 3D Point Cloud, LiDAR Point, LiDAR Point Clouds, Percentile Scores, 3D Detection, Semi-supervised Learning, Different Amounts Of Data, Object Bounding Boxes

https://doi.org/10.48550/arXiv.2202.07028

Chan Hee Song, Jihung Kil, Tai-Yu Pan, Brian Sadler, Wei-Lun Chao, Yu Su

Imageomics

https://github.com/chanhee-luke/M-Track

Imageomics, Artificial Intelligence, Computation and Language, Computer Vision, Pattern Recognition, Machine Learning, Robotics

https://i2insights.org/2022/07/12/generating-cross-disciplinary-projects/

Gemma Jiang

Imageomics

Team Science, Communication, Processes, Teamwork, Cross-disciplinarity, Problem framing

https://doi.org/10.48550/arXiv.2202.11124

Cheng Zhang, Tai-Yu Pan, Tianle Chen, Jike Zhong, Wenjin Fu, Wei-Lun Chao

Imageomics

Imageomics, Computer Vision, Pattern Recognition

https://link.springer.com/chapter/10.1007/978-3-031-39141-5_15

Dom Jebbia, Xioajun Wang, Yasin Bakis, Henry Bart, Jane Greenberg

Imageomics

Imageomics, Metadata pipelines, Open data, Metadata workflows, FAIR data, Digital images, Biodiversity Collections

https://doi.org/10.1371/journal.pone.0278035

Chi Zhang, Arthur Porto, Sara Rolfe, Altan Kocatulum, Murat Maga

Imageomics

https://github.com/SlicerMorph/Mouse_Models

https://github.com/SlicerMorph/Mouse_Models/tree/main/Models

Imageomics, csv-to-json, slicer, slicermorph

https://doi.org/10.1371/journal.pone.0278522

Kaiya Provost, Jiaying Yang, Bryan Carstens

Imageomics

github.com/kaiyaprovost/bioacoustics

https://doi.org/10.5061/dryad.8pk0p2nrb

Imageomics, vocalizations, Evolutionary Biology, birds, avian, Machine Learning, Ecology

https://doi.org/10.1242/bio.059698

Sara Rolfe, Sophie Whikehart, Murat Maga

Imageomics

https://github.com/SlicerMorph/SlicerMEMOS

http://www.mouseimaging.ca/technologies/mouse_atlas/mouse_embryo_atlas.html

Imageomics, csv-to-json, slicer, slicermorph, Segmentation, Deep learning, Embryo, Micro-CT, Mouse, Automated

https://i2insights.org/2023/03/21/organizing-research-coordination-meetings/

Gemma Jiang, Diane Boghrat, Jenny Grabmeier

Imageomics

Team Science, Communication, Processes, Teamwork, Cross-disciplinarity, Facilitation, Meeting protocols

http://rave.ohiolink.edu/etdc/view?acc_num=osu168198420667979

Reshma Ramesh Babu, Wei-Lun Chao, Tanya Berger-Wolf

Imageomics

https://github.com/Imageomics/Butterfly-mimicry

Biology, Computer Science, Conservation, Ecology, Genetics, Imageomics, Butterflies, Mimicry, Machine Learning, Computer Vision, Traits

https://doi.org/10.48550/arXiv.2306.03228

Mohannad Elhamod, Mridul Khurana, Harish Babu Manogaran, Josef Uyeda, Meghan Balk, Wasila Dahdul, Yasin Bakis, Henry Bart, Paula Mabee, Hilmar Lapp, James Balhoff, Caleb Charpentier, David Carlyn, Wei-Lun Chao, Charles Stewart, Daniel Rubenstein, Tanya Berger-Wolf, Anuj Karpatne

Imageomics

https://github.com/elhamod/phylonn

Imageomics, Segmentation, Deep learning, Embryo, Micro-CT, Mouse, Automated

https://doi.org/10.1101/2023.03.08.531720

Jiaying Yang, Bryan C. Carstens, Kaiya L. Provost

Imageomics

https://datadryad.org/dataset/doi:10.5061/dryad.tx95x6b4j

Imageomics, bioacoustics, bird song, climate, cultural drift, Machine Learning, Zonotrichia leucophrys

https://doi.org/10.1093/iob/obad024

Chi Zhang, Murat Maga

Imageomics

https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/iob/5/1/10.1093_iob_obad024/1/obad024_supplemental_files.zip?Expires=1774453788&Signature=ZaTVIyVfbEjoekt668VJxqwrCiyEVJ2Vs3Eu~Qmv7NuwqSBjSIEmZm4XUxP~ri4x1BIiuxkZLhadgNH7GzBFE6Pvm-FHVj~CDr2nmxaHw-PZARkmZvKZBtQTJVLmp7Yc52tZOm85PK6~88rKeltJYFYfqLMjC-PvvVQ4dgcrGfK6os5L-u8T7IidZIk2Ey6Nf5Y4zvi15Ak5rO~wP4ZcSIz7IHxx44fjSvRzCGBnG8zUfQnJokgUtsTNdxkU0xEKLyQjXFSvMJpULG0qW9scJ3VzBucwBYI3IHAHaQ7TY-PFvxLAgAWKaHochvztM0PEmFcr~GuK7m00uNGeDTfZWw__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA

Imageomics, Photogrammetry, OpenDroneMap, 3D morphometrics

https://doi.org/10.3389/frma.2023.1211554

Gemma Jiang, Diane Boghrat, Jenny Grabmeier, Jennifer E Cross

Imageomics

Team Science, Cross-disciplinary, Leadership

https://scholar.google.com/citations?view_op=view_citation&hl=en&user=axVWN84AAAAJ&sortby=pubdate&citation_for_view=axVWN84AAAAJ:e_rmSamDkqQC

Yasin Bakış, Xiaojun Wang, Bahadır Altıntaş, Dom Jebbia, Henry Bart

Imageomics

Imageomics, biodiversity informatics, data management, machine learning, artificial intelligence, datawrangling

https://i2insights.org/2023/09/12/organizing-all-hands-meetings/

Gemma Jiang, Diane Boghrat, Jenny Grabmeier

Imageomics

Team Science, Processes, Teamwork, Meeting protocols, Team roles

https://proceedings.neurips.cc/paper_files/paper/2023/hash/5d087955ee13fe9a7402eedec879b9c3-Abstract-Conference.html

Cheng-Hao Tu, Hong-You Chen, Zheda Mai, Like Zhong, Vardaan Pahuja, Tanya Berger-Wolf, Song Gao, Charles Stewart, Yu Su, Wei-Lun Chao

Imageomics

Imageomics, Machine Learning, Pre-trained source model

https://par.nsf.gov/servlets/purl/10530238

Jenna Kline, Christopher Stewart, Tanya Berger-Wolf, Michelle Ramirez, Samuel Stevens, Reshma Ramesh Babu, Namrata Banerji, Alec Sheets, Sowbaranika Balasubramaniam, Elizabeth Campolongo, Matthew Thompson, Charles Stewart, Maksim Kholiavchenko, Daniel Rubenstein, Nina Van Tiel, Jackson Miliko

Imageomics

https://github.com/Imageomics/kabr-tools

https://huggingface.co/datasets/imageomics/KABR

autonomous flight, UAVs, ecology, Machine Learning, Computer Vision, imageomics

https://openaccess.thecvf.com/content/WACV2024W/CV4Smalls/papers/Kholiavchenko_KABR_In-Situ_Dataset_for_Kenyan_Animal_Behavior_Recognition_From_Drone_WACVW_2024_paper.pdf

Maksim Kholiavchenko, Jenna Kline, Michelle Ramirez, Sam Stevens, Alec Sheets, Reshma Babu, Namrata Banerji, Elizabeth Campolongo, Matthew Thompson, Nina Van Tiel, Jackson Miliko, Eduardo Bessa, Isla Duporge, Tanya Berger-Wolf, Daniel Rubenstein, Charles Stewart

Imageomics

https://dirtmaxim.github.io/kabr

Imageomics, behavior, code, data, kabr, mini-scenes, models, pipelines, tools, ungulates

https://doi.org/10.1101/2024.02.11.579809

Sydney Decker, Kaiya Provost, Bryan Carstens

Imageomics

https://github.com/skdecker/PhylogeographicBreaks

Imageomics, bats, birds, dispersal, macrogenetics, Monmonier’s algorithm, phylogeography, Random Forests

https://doi.org/10.1111/2041-210X.14327

Meghan Balk, John Bradley, M. Maruf, Bahadir Altintaş, Yasin Bakiş, Henry Bart, David Breen, Christopher Florian, Jane Greenberg, Anuj Karpatne, Kevin Karnani, Paula Mabee, Joel Pepper, Dom Jebbia, Thibault Tabarin, Xiaojun Wang, Hilmar Lapp

Imageomics

https://zenodo.org/records/10629836

Imageomics, computational reproducibility, FAIR, image data, imageomics, Machine Learning, workflowautomation

https://link.springer.com/article/10.1007/s11263-024-02071-1

Ekaterina Nepovinnykh, Ilia Chelak, Tuomas Eerola, Veikka Immonen, Heikki Kälviäinen, Maksim Kholiavchenko, Charles Stewart

Imageomics

https://github.com/kwadraterry/Norppa

https://doi.org/10.23729/0f4a3296-3b10-40c8-9ad3-0cf00a5a4a53

Imageomics, Computer Vision, Image processing, Animal biometrics, Re-identification, Ringed seals, Convolutional neural networks

https://doi.org/10.48550/arXiv.2405.17698

Isla Durporge, Maksim Kholiavchenko, Roi Harel, Scott Wolf, Dan Rubenstein, Meg Crofoot, Tanya Berger-Wolf, Stephen Lee, Julie Barreau, Jenna Kline, Michelle Ramirez, Charles Stewart

Imageomics

https://dirtmaxim.github.io/BaboonLand

https://huggingface.co/datasets/imageomics/BaboonLand

Imageomics, Video, imbalanced, conservation, annotated video, object-detection, annotation, UAV, Kenya, behavior recognition, drone, video, animal behavior, baboons, pandas, Mpala Research Centre

https://doi.org/10.1101/2024.05.22.595350

Oshane Thomas, Murat Maga

Imageomics

https://github.com/oothomas/SSC-MorphVQ

https://github.com/oothomas/SSC-MorphVQ/tree/master/data

Imageomics, functional map framework; geometric Morphometrics; geometry processing; landmarking; mouse mandible; rapid morphological phenotyping.

https://doi.org/10.48550/arXiv.2311.04157

Dipanjyoti Paul, Arpita Chowdhury, Xinqi Xiong, Feng-Ju Chang, David Carlyn, Samuel Stevens, Kaiya Provost, Anuj Karpatne, Bryan Carstens, Daniel Rubenstein, Charles Stewart, Tanya Berger-Wolf, Yu Su, Wei-Lun Chao

Imageomics

https://github.com/Imageomics/INTR

https://github.com/Imageomics/INTR/tree/main/datasets

Imageomics, images, butterflies, interpretable, birds, cross-attention, CV, animals, image classification, biology, transformers, computer vision, explainable ai, fine-grained classification, imageomics, interpretation, transformer

https://jennamk14.github.io/images/Integrating%20Biological%20Data%20into%20Autonomous%20Remote%20Sensing%20Systems%20for%20In%20Situ%20Imageomics-%20A%20Case%20Study%20for%20Kenyan%20Animal%20Behavior%20Sensing%20with%20Unmanned%20Aerial%20Vehicles%20(UAVs).pdf

Jenna Kline, Maksim Kholiavchenko, Otto Brookes, Tanya Berger-Wolf, Charles Stewart, Christopher Stewart

Imageomics

Imageomics, drone, ecology, zebra, Grevy's zebra, conservation, UAV, telemetry