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https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction

Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery
https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction

image-processing lightsheet machine-learning microscopy neuroscience nextflow-pipelines pipeline segmentation

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Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

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README 

        
# ExLLSM Circuit Reconstruction Pipeline



[![Cite with Zenodo](https://zenodo.org/badge/323991895.svg)](https://zenodo.org/badge/latestdoi/323991895)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.1-23aa62.svg)](https://www.nextflow.io/)

[![Run with Docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/)

[![Run with Singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/)



This is a pipeline, described in [this research article]( https://doi.org/10.7554/eLife.81248), intended for analyzing expansion lattice light-sheet microscopy (ExLLSM) data, consisting of several independent workflows, and integration with [VVD Viewer](https://github.com/takashi310/VVD_Viewer).



## Quick Start



The only software requirements for running this pipeline are [Nextflow](https://www.nextflow.io) (version 20.10.0 or greater) and [Singularity](https://sylabs.io) (version 3.5 or greater). If you are running in an HPC cluster, ask your system administrator to install Singularity on all the cluster nodes.



To [install Nextflow](https://www.nextflow.io/docs/latest/getstarted.html):



    curl -s https://get.nextflow.io | bash 



Alternatively, you can install it as a conda package:



    conda create --name exm -c bioconda nextflow



To [install Singularity](https://sylabs.io/guides/3.7/admin-guide/installation.html) on CentOS Linux:



    sudo yum install singularity



Clone the expansion microscopy pipeline repository with the following command:



    git clone https://github.com/JaneliaSciComp/expansion-microscopy-pipeline.git



Before running the pipeline for the first time, run setup to pull in external dependencies:



    ./setup.sh



You can now launch a pipeline, e.g.:



    ./stitch_pipeline.nf [arguments]



## Pipeline Overview



This pipeline is containerized and portable across the various platforms supported by [Nextflow](https://www.nextflow.io). So far it has been tested on a standalone Linux workstation and the LSF cluster at Janelia Research Campus. If you run it successfully on any other platform, please let us know so that we can update this documentation.



The pipeline includes the following workflows:



* **[Stitching](docs/Stitching.md)** - distributed stitching pipeline including flatfield correction and deconvolution

* **[Image Processing](docs/ImageProcessing.md)** - file conversion, Fiji macros for cropping, cross-talk subtraction, thresholding, and more

* **[Neuron Segmentation](docs/NeuronSegmentation.md)** - workflows for neuron segmentation

* **[Synapse Prediction](docs/SynapsePrediction.md)** - workflows to detect and quantify synaptic sites within and connections between neurons



## Pipeline Execution



### Run the pipeline locally



To run the pipeline locally, you can use the standard profile:



    ./main.nf [arguments]



### Run the pipeline on IBM Platform LSF



To run this pipeline in distributed mode on a cluster, all input and output paths must be mounted and accessible on all the cluster nodes.



Edit `nextflow.config` to create a profile for your local environment. A profile for the Janelia Compute Cluster is provided and can be used like this:



    ./main.nf -profile lsf --lsf_opts "-P project_code" [arguments]



Usage examples are available in the [examples](examples) directory.



## User Manual



Further detailed documentation is available here:



* [General Parameters](docs/Parameters.md)

* Workflows

  * [Stitching](docs/Stitching.md)

  * [Image Processing](docs/ImageProcessing.md)

  * [Neuron Segmentation](docs/NeuronSegmentation.md)

  * [Synapse Prediction](docs/SynapsePrediction.md)

* [Troubleshooting](docs/Troubleshooting.md)

* [Development Guide](docs/Development.md)



## Related Repos



These other repositories contain code bases developed in conjuction with this pipeline. They are cloned during the Docker container build step.



* [exllsm-synapse-detector](https://github.com/JaneliaSciComp/exllsm-synapse-detector)

* [exllsm-neuron-segmentation](https://github.com/JaneliaSciComp/exllsm-neuron-segmentation)

* [exllsm-fiji-plugins](https://github.com/JaneliaSciComp/exllsm-fiji-plugins)



## Open Source License



This software is made available under [Janelia's Open Source Software](https://www.janelia.org/open-science/software-licensing) policy which uses the BSD 3-Clause License.