Published March 29, 2024
| Version v1
Software
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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)
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md5:433ba19412678208c63690262a0e36f9
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99.9 MB | Preview Download |
md5:cf5bfb94ecc509c36967d0002047088d
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11.9 GB | Download |