SikuliX

SikuliX automates image-based control and scripting to enable automated spatially targeted optical micro proteomics (autoSTOMP) workflows.

Key Features:

• Image Recognition (OpenCV): Uses OpenCV-based image recognition to detect visual elements for programmatic control and automation.
• Scriptable Automation: Provides customizable automation scripts to orchestrate protocol steps for STOMP/autoSTOMP workflows.
• Software Integration: Automates communication between Zeiss Zen Black imaging software and FIJI image processing software.
• Tile Array Creation: Automates creation and organization of tile arrays across fields of view for systematic sampling.
• Autofocus and Image Capture: Automates autofocus and consistent image acquisition during confocal microscopy sessions.
• Photo-tagging Modification: Enables targeted photo-tagging of specific subcellular structures for photo-driven crosslinking.

Scientific Applications:

• Spatially Targeted Optical Micro Proteomics (STOMP/autoSTOMP): Enables region-specific proteome analysis using confocal microscopy and photo-driven crosslinking.
• Crosslinker-based Purification: Supports protocols using biotin-benzophenone crosslinker and endogenous biotin blocking to facilitate purification with magnetic streptavidin beads.
• Mass Spectrometry Identification: Facilitates labeling and downstream purification compatible with standard LC-MS/mass spectrometry workflows for protein identification.
• Subcellular Resolution: Applicable to labeling and analysis of structures as small as 1–2 μm in diameter.
• Demonstrated Sample Types: Applied to human foreskin fibroblasts and mouse bone marrow-derived dendritic cells infected with Toxoplasma gondii.

Methodology:

Uses OpenCV-based image recognition to automate interactions and communication between Zeiss Zen Black and FIJI, including automated tile array creation, autofocus and image capture, and targeted photo-tagging modifications.