scripted render pipeline

Automated Python pipeline for processing volume electron microscopy (EM) and integrated correlative light and electron microscopy (CLEM) datasets, interfacing with the render-ws rest api. scripted-render-pipeline is configured to process (correlative) array tomography datasets in formats from FAST-EM, a multibeam scanning transmission electron microscope, and SECOM, an optical microscope for integrated correlative light and electron microscopy.

The following is currently supported:

Automated post-correction (FAST-EM datasets only)
Import to render-ws (FAST-EM and SECOM datasets)
Export to (self-managed) WebKnossos instances (FAST-EM and SECOM datasets).

This repository is tied to the interactive render workflow, which covers (supervised) 2D stitching and 3D alignment of FAST-EM data. The modules in the scripted-render-pipeline can be used in the interactive-render-workflow.

Requirements

Server with Linux distribution (Ubutuntu) and decent computation power (>128 GB RAM, >40 CPU cores).
render-ws installation (setup instructions)
Local WebKnossos instance (setup instructions). Since we are using a self-hosted WebKnossos instance, export to the Remote WebKnossos is currently not supported be can be considered on request.

Installation

This instruction assumes that git and Python are installed. Moreover, it is recommended to install the software in a Python virtual environment. Python 3.10 and later versions are supported. Clone the repository into a suitable target directory and install with pip:

git clone https://github.com/hoogenboom-group/scripted-render-pipeline
pip install --require-virtualenv .

this will install required dependencies from PyPI as well

Usage

render_import for importing to render

render_export for exporting to CATMAID or WebKnossos

render_basic_auth {show,save} for managing http basic auth credentials

post_correct for post-corrrecting FAST-EM images (prior to import)

Each module has a main.py file which executes the code when called from the command line using the commands listed above. Dataset and processing parameters can be set in this file.

Usage as module

python -m scripted_render_pipeline.importer for importing to render

python -m scripted_render_pipeline.basic_auth {show,save} for managing http basic auth credentials

python -m scripted_render_pipeline.exporter for exporting to WebKnossos

Support

This software is developed for scientific research projects at Delft University of Technology and is released with no fixed update schedule. The software is under active development and thus significant changes to the structure and functionality can be expected.

hoogenboom-group / scripted-render-pipeline