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Data Dictionary

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Chris Churas edited this page Dec 7, 2017 · 12 revisions

Package

Defined as the set of 16 hdf5 image files each containing the stack of images perturbed 16 different ways.

Toggle table of contents Pages 43

Home
Add Validation to training
Breakdown of CloudFormation Template
Breakdown of Resources section of CloudFormation Template
caffepredict.sh
caffetrain.sh
Check and increase AWS EC2 limits
CreateTrainJob.m
Creating Cdeep3M Release
Data Dictionary
Datasets and trained models preloaded on CDeep3M via Amazon AWS Cloud
Demorun 1 Running prediction with pre trained model
Demorun 2 Running small training and prediction with mito testsample dataset
Developer topics
Disclaimer
Download datasettwo
EC2 Resource Type
Finding Deep Learning AMI
Format of h5 augmented training data
Format of input image training data
How CDeep3M release system works
How to access CDeep3M cloud
How to import key pair into us west 2 region
How to retrain a pretrained network
How to troubleshoot CloudFormation template
Launching CDeep3m via AWS CloudFormation
Linux IMOD install instructions
Mac IMOD install instructions
PreprocessTrainingData.m
Prototype AWS command line invocation
Run CDeep3M training and prediction
runprediction.sh
runtraining.sh
S3 buckets needed for release
Shutting down CDeep3M AWS CloudFormation
Speed up
trainworker.sh
Tutorial 1 Generating training data with IMOD
Tutorial 2 Launch and train CDeep3M
Tutorial 3 Run CDeep3M
Tutorial 4 Post processing of Automatically Generated Segmentations
Tutorial required tools
Windows IMOD install instructions

Launching CDeep3m via AWS CloudFormation

NBCR Training Tutorial 1

NBCR Training Tutorial 2

NBCR Training Tutorial 3

NBCR Training Tutorial 4

Developer topics

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