• List of docker containers
• DockerHub

List of docker containers

We hereafter list the docker containers, their use and list the installed libraries:

Progress:

• DB
• Scanner
• SmartInterpreter
• VirtualScanner
• Visualizer

DB

The database container.

Aim

Gather the acquired images, reconstructed plants architectures & quantitative data.

Docker

FROM continuumio/miniconda3

Dependencies:

Internal dependencies:

• data-storage

External dependencies:

• opencv ??

Scanner

The database container.

Aim

Gather the acquired images, reconstructed plants architectures & quantitative data

FROM continuumio/miniconda3

Dependencies:

Internal dependencies:

• data-storage, the database API, as well as classes for data processing using luigi.

External dependencies:

• lettucethink-python, python tools and controllers for the lettucethink robot.

SmartInterpreter

The reconstruction and quantification container.

Aim

Gather the algorithms and processing pipelines to extract quantitative biological information on plants architecture from a set of photo acquisition.

FROM colmap/colmap

Dependencies:

Internal dependencies:

• data-storage, the database API, as well as classes for data processing using luigi.
• Segmentation, virtual plant segmentation methods using 2D images generated from the virtual scanner and neural networks.
• cgal_bindings_skeletonization, Python CGAL bindings for skeletonization.
• Scan3D, the elements used to run 3D scan of individual plants.

External dependencies:

• Open3D is mostly used for IO and data structures.
• Colmap is used for Structure From Motion reconstruction.
• cgal is used for skeletonization. TO REMOVE ?!

VirtualScanner

The virtual scanner container.

Aim

Gather the tools to create virtual plants and render realistic snapshots.

FROM alpine:3.10

Dependencies:

Internal dependencies:

• data-storage, the database API, as well as classes for data processing using luigi.

External dependencies:

• blender
• lpy

Visualizer

The plant visualizer.

Webapp that dialog with the database to display images & some quantitative traits.

FROM alpine:3.10

Dependencies:

Internal dependencies:

• data-storage, the database API, as well as classes for data processing using luigi.

External dependencies:

• sony_visualiseur-plantes-3d

Notes: scanner-rest-api & npm start are two distinct process to start !

DockerHub

Colmap

Docker images for the COLMAP open source project:

https://hub.docker.com/r/colmap/colmap

nvidia/cuda with colmap - (compatible with Driver Version: 418.67 CUDA Version: 10.1)

https://hub.docker.com/r/geki/colmap