VLab4Mic supplementary data

Supplementary data for VLab4Mic: A Virtual Laboratory for Microscopy About this dataset This dataset contains 2 cusom models in CIF format, one for a Clathrin Coated Structure for a dome, and another as a flat lattice. Dome and flat clathrin coated structures were modelled in ChimeraX by manually placing copies of the triskelion structure 6WCJ and 3LVH, respectively. The triskelions were placed and reoriented manually. The resulting model was exported as a CIF file and used as input for VLab4Mic simulations. VLab4Mic: A Virtual Laboratory for Microscopy VLab4Mic is a friendly toolkit to help researchers simulate fluorescence microscopy images, no coding required. VLab4Mic lets you explore, test, and validate imaging experiments before stepping into the microscope room. Whether you are new to Python or an experienced bioimage researcher, VLab4Mic provides a safe sandbox to: - Build virtual samples from PDB/CIF structures - Apply direct or indirect fluorescent labeling - Introduce Structural integrity, crowding, and structural variation - Simulate image acquisition across modalities - Run parameter sweeps to explore experimental conditions - Compare noiseless vs. realistic acquisitions Who Is This Tool For? - New microscopy users: to gain intuitive understanding without coding - Researchers designing experiments: testing probes, PSFs, exposure times - Microscopy experts: benchmarking reconstruction methods or PSFs Core Features ✔ Structural modelling ✔ Virtual sample creation ✔ Imaging simulations ✔ Parameter sweeps ✔ Widget-based GUI ✔ Flexible Python API Quick Start Options Example 1: Google Colab (No Installation Needed) The easiest way to start. Click to open the corresponding notebook. ✔ No installation ✔ No configuration ✔ Works in browser ✔ Always up to date Category Description Notebook Colab Main Interface Create virtual samples & simulate imaging VLab4Mic_main VLab4Mic_main Parameter Sweeps Configure & run simulation sweeps VLab4Mic_parameter_sweeps VLab4Mic_parameter_sweeps Find further examples and usage in VLab4Mic github repository.