Published March 29, 2024 | Version v1
Software Open

Docker container for DELiVR pipeline (training, version 6.04)

  • 1. Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Munich

Description

Initial Release of the docker containers for the DELiVR cleared-brain analysis pipeline, as described in our 2024 publication: 

Virtual reality-empowered deep-learning analysis of brain cells

Kaltenecker, Al-Maskari, Negwer, et al., Nature Methods 2024

https://doi.org/10.1038/s41592-024-02245-2

This repository contains the training container: 

  • This container is based on the github repository https://github.com/erturklab/delivr_train
  • The pipeline in this container requires annotated 3D stacks (preferably annotated in VR as it's faster) as training data. 
  • The training pipeline can be started via the FIJI plugin or by the "docker run" command
  • Please refer to the handbook accompanying the publication for details. 

As a proof-of-concept, we include the training data used to train the c-fos model.

Files

cFos_training_data.zip

Files (12.0 GB)

Name Size Download all
md5:433ba19412678208c63690262a0e36f9
99.9 MB Preview Download
md5:cf5bfb94ecc509c36967d0002047088d
11.9 GB Download