diff --git a/datasets/chammi.yaml b/datasets/chammi.yaml new file mode 100644 index 000000000..fc2e61a41 --- /dev/null +++ b/datasets/chammi.yaml @@ -0,0 +1,61 @@ +Name: CHAMMI-75 +Description: | + Quantifying cell morphology using images and machine learning models has proven to be a powerful tool to study the response of cells to treatments. + However, the models used to quantify cellular morphology are typically trained with a single microscopy imaging type and under controlled experimental conditions. + This results in specialized models that cannot be reused across biological studies because the technical specifications do not match (e.g., different number of channels), + or because the target experimental conditions are out of distribution. We have created CHAMMI-75, a large-scale dataset containing 2.8 million multi-channel, + high-resolution images curated from 75 diverse, publicly available biological studies. This dataset is useful to investigate and develop channel-adaptive models, + which could process microscopy images of varying technical specifications and regardless of the number of channels. By breaking the limitations of existing models, + CHAMMI-75 is an invaluable resource for creating the next generation of foundation models for image-based biological research. +Documentation: https://github.com/CaicedoLab/CHAMMI-75 +Contact: Contact via email Juan Caicedo, juan.caicedo@wisc.edu +ManagedBy: Morgridge Institute for Research +UpdateFrequency: Every 2 years +Tags: + - microscopy + - machine learning + - biology + - life sciences + - imaging + - high-throughput imaging + - cell imaging + - fluorescence imaging +License: CC BY 4.0 License +Citation: +Resources: + - Description: Images, training set and evaluation set available in an S3 bucket + ARN: + Region: + Type: + Explore: +DataAtWork: + Tutorials: + - Title: Get To Know A Dataset: CHAMMI-75 + URL: https://github.com/CaicedoLab/CHAMMI-75/blob/main/aws-tutorials/ + NotebookURL: https://github.com/CaicedoLab/CHAMMI-75/blob/main/aws-tutorials/get-to-know-a-dataset-template.ipynb + AuthorName: Vidit Agrawal, Juan Caicedo + AuthorURL: + Services: Getting to know a dataset + - Title: Running CHAMMI-75 Evaluation Benchmarks + URL: https://github.com/CaicedoLab/CHAMMI-75/blob/main/aws-tutorials/ + NotebookURL: https://github.com/CaicedoLab/CHAMMI-75/blob/main/aws-tutorials/running-benchmarks.ipynb + AuthorName: Vidit Agrawal, Juan Caicedo + Author URL: + Services: It will enable researchers to run state of the art benchmarks in the exploration of single cell self-supervised learning foundation models. + Tools & Applications: + - Title: CHAMMI-75 Source Code + URL: https://github.com/CaicedoLab/CHAMMI-75 + AuthorName: Vidit Agrawal + AuthorURL: + - Title: CHAMMI Benchmarking Source Code + URL: https://github.com/chaudatascience/channel_adaptive_models + AuthorName: Chau Pham + AuthorURL: + Publications: + - Title: CHAMMI: A benchmark for channel-adaptive models in microscopy imaging + URL: https://neurips.cc/virtual/2023/poster/73620 + AuthorName: Zitong Sam Chen, Chau Pham, Siqi Wang, Michael Doron, Nikita Moshkov, Bryan Plummer, Juan C. Caicedo + AuthorURL: +DeprecatedNotice: +ADXCategories: + - Healthcare & Life Sciences Data