asem-project.yaml

Name: Automated Segmentation of Intracellular Substructures in Electron Microscopy (ASEM) on AWS
Description: The Automated Segmentation of intracellular substructures in Electron Microscopy (ASEM) project provides deep learning models trained to segment structures in 3D images of cells acquired by Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). Each model is trained to detect a single type of structure (mitochondria, endoplasmic reticulum, golgi apparatus, nuclear pores, clathrin-coated pits) in cells prepared via chemically-fixation (CF) or high-pressure freezing and freeze substitution (HPFS). You can use our open source pipeline to load a model and predict a class of sub-cellular structures in naive FIB-SEM cells images. If required, a fine-tuning procedure allows a model to be trained on a small amount of additional ground truth annotations to improve a prediction on a naive dataset. Together with the trained models, we also provide the training, validation and test datasets.
Documentation: https://open.quiltdata.com/b/asem-project
Contact: tklab@tklab.hms.harvard.edu
ManagedBy: Kirchhausen Lab at Harvard Medical School
UpdateFrequency: Data is added as it becomes available
Tags:
  - aws-pds
  - biology
  - cell biology
  - segmentation
  - microscopy
  - electron microscopy
  - computer vision
  - imaging
License: All available datasets and models are licensed under a Creative Commons Attribution-ShareAlike 4.0 International License
Resources:
  - Description: High resolution 3D cell image datasets
    ARN: arn:aws:s3:::asem-project/datasets/
    Region: us-east-1
    Type: S3 Bucket
  - Description: Trained ML segmentation models for use in ASEM pipeline
    ARN: arn:aws:s3:::asem-project/models/
    Region: us-east-1
    Type: S3 Bucket
DataAtWork:
  Tutorials:
    - Title: Data layout and how to view
      URL: https://open.quiltdata.com/b/asem-project
      AuthorName: kirchhausenlab
      AuthorURL: https://github.com/kirchhausenlab
    - Title: How to use models
      URL: https://github.com/kirchhausenlab/incasem/blob/main/README.md
      AuthorName: kirchhausenlab
      AuthorURL: https://github.com/kirchhausenlab/incasem/blob/main/README.md
  Tools & Applications:
    - Title: ASEM Colab Notebook (Interactive Demo)
      URL: https://colab.research.google.com/drive/1FgRKN2mM6x18S02Qe4XMyxFeFubZxaMw
      AuthorName: Patrick Stock
      AuthorURL: https://github.com/patrickstock
    - Title: TK Lab Data Explorer
      URL: http://asem-viewer-env.eba-rrnvmfwa.us-east-1.elasticbeanstalk.com/
      AuthorName: Patrick Stock
      AuthorURL: https://github.com/patrickstock
  Publications:
    - Title: Deep neural network automated segmentation of cellular structures in volume electron microscopy
      URL: https://rupress.org/jcb/article-pdf/222/2/e202208005/1444783/jcb_202208005.pdf
      AuthorName: Benjamin Gallusser, Giorgio Maltese, Giuseppe Di Caprio, Tegy John Vadakkan, Anwesha Sanyal, Elliott Somerville, Mihir Sahasrabudhe, Justin O’Connor, Martin Weigert, Tom Kirchhausen