Table 2.
EXACT documentation and references for the corresponding sections and supplementary videos.
| Section: Architecture | |
| docker-compose.prod.yml | Setup EXACT via Docker with the command |
| docker-compose -f docker-compose.prod.yml up -d –build | |
| Supplementary Video S10 | EXACT installation guide with Docker |
| Section: Application tier | |
| models.py | Saves information to the database or file system |
| views.py | Creates HTML views for the presentation tier |
| serializers.py | Serialises data for the REST-API |
| api_views.py | Provides database CRUD operations via the REST-API |
| doc/train_object_detection.ipynb | Code to train an object detection model via the REST-API |
| urls.py | Handles the mapping between URLs and python functions |
| exact/images | The images module is responsible for all image-based CRUD operations |
| Supplementary Video S7 | How to create image sets and upload images |
| Supplementary Video S8 | Explain image set details |
| exact/annotation | The annotation module is responsible for all CRUD operations regarding annotations, verification, media files and the annotation versioning system |
| exact/plugin | The plugin module handles analysis or visualisation plugins |
| exact/users | The users module handles the CRUD operations for users and teams |
| Supplementary Video S14 | How to setup user access rights |
| exact/datasets | The datasets module provides features to automatically download and setup predefined data sets with their annotations |
| exact/datasets/templates | Folder containing data set HTML templates |
| exact/datasets/views.py | Implements functions to setup predefined data sets within EXACT |
| Supplementary Video S5 | How to setup and use a demo data set |
| Section: Inference | |
| doc/Inference Asthma.ipynb | A REST-API inference example |
| Supplementary Video S9 | Example for REST-API and JavaScript inference |
| Section: Annotation map screening mode | |
| doc/AnnotationMap.ipynb | Code to create annotation maps |
| Supplementary Video S2 | How to create annotation maps |
| doc/ClusterCells.ipynb | Code to cluster Asthma cells |
| Supplementary Video S4 | How to cluster Asthma cells |
| Section: Image set versioning and machine learning support | |
| doc/DownloadStudyAnnotations.ipynb | Code to download annotations from EXACT |
| Supplementary Video S15 | How to create a new image set version and track changes |
| Section: Annotation templates | |
| Supplementary Video S3 | How to create annotation templates with EXACT |
| Section: Pathology annotation study | |
| Supplementary Video S1 | How to download annotations and explanation of parts of the annotation study |
| doc/DownloadStudyAnnotations.ipynb | Code to download annotations via the REST-API |
| Section: Multi-species pulmonary hemosiderophages cytology data set | |
| Supplementary Video S6 | How to create density maps and explanation of the EIPH plugin |
| doc/Create_DensityWSI-Equine.ipynb | Source code for density maps |
| Section: Skin tumour tissue quantification | |
| doc/SyncImageAndAnnotations.ipynb | Code to synchronise between SlideRunner and EXACT |
| Supplementary Video S12 | How to synchronise between SlideRunner and EXACT |
| Supplementary Video S11 | How to segment with EXACT |
| doc/Segmentation.ipynb | Code to download information from EXACT to train a segmentation network |
| doc/PatchClassifier.ipynb | Code to download information from EXACT to train a patch classifier |
| Section: Clustering and visualisation of killer whale sounds | |
| Supplementary Video S13 | How to perform sound clustering and visualisation |