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. Developed by @thopp-tudelft, @lanery and @arentkievits.

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 software currently supports automated post-correction of FAST-EM datasets, import to render-ws and export to (self-managed) WebKnossos instances. More functionalities will be added in later stages.