Examples¶
Ready-to-run example scripts demonstrating common VLab4Mic workflows. Before running, make sure you have installed VLab4Mic.
Run any script with:
Available Scripts¶
| Category | Description | Script |
|---|---|---|
| Image virtual sample | Create a virtual sample and simulate its imaging acquisition |  |
| Parameter sweep | Set up and run a parameter sweep analysis | |
| Real vs Simulation | Create a simulated image based on a real experimental image | |
| Custom structure | Image a virtual sample using a custom local PDB/CIF file | |
Article Figure Scripts¶
Scripts used to generate the figures in the VLab4Mic publication. Each script is self-contained and demonstrates a specific feature or validation scenario.
| Figure | Description | Script |
|---|---|---|
| Fig. 1 | HIV capsid (3J3Y) imaged across all modalities | |
| Fig. 2 | NPC (7R5K) panel with SMLM and quantification | |
| Fig. 3 (A–C) | Parameter sweep panels for structural comparison | |
| Fig. 3 (D–E) | Parameter sweep with labelling efficiency | |
| Fig. 4 | Clathrin-coated structure (CCS) imaging | |
| Fig. S — AlphaFold | Using a locally downloaded AlphaFold model as input structure | |
| Fig. S — Depth of field | Effect of depth-of-field parameter on simulated images | |
| Fig. S — Image positioning | Using a reference image to position epitopes in the virtual sample | |
| Fig. S — Labelling efficiency & hindrance | Labelling efficiency and steric hindrance effects | |
| Fig. S — SMLM localisation (CCS) | Localisation table simulation for clathrin-coated structures | |
| Fig. S — Multicolour | Two-colour imaging of the same structure with different probes | |
| Fig. S — Multiple structures | Imaging multiple different structures in the same field of view | |
| Fig. S — NPC quantification | NPC ring quantification simulation | |
| Fig. S — Primary & secondary | Indirect labelling with primary and secondary antibody models | |
| Fig. S — Probe examples | Gallery of all probe templates across different structures | |
| Fig. S — Site-specific labelling | Site-specific probe conjugation on a defined residue | |
| Fig. S — Structural integrity | Structural integrity parameter effects on NPC and capsid | |
| Fig. S — Structure normals | Structure normal directions and probe positioning | |
| Fig. S — Structure parsing | Structure parsing, asymmetric units, and multiple targets | |
Image Virtual Sample¶
Demonstrates the core image_vsample function. In this example, 10 Nuclear Pore Complexes (NPC, model 7R5K) are labelled at the C-terminal of Nup96 and imaged across multiple modalities.
Key things shown: - Selecting a structural model from PDB - Using a pre-configured probe template - Simulating acquisition across Widefield, Confocal, STED, and SMLM
Parameter Sweep¶
Demonstrates run_parameter_sweep. In this example, labelling efficiency and structural integrity are swept across 3 values each (9 combinations total), and each output is compared against a reference image via Pearson correlation.
Key things shown: - Configuring sweep parameters as lists or ranges - Running repeated simulations - Generating heatmap analysis outputs
Real vs Simulation¶
Shows how to base a simulated image on the parameters estimated from a real experimental acquisition — useful for validation and benchmarking.
Custom Structure¶
Shows how to load and use a local PDB or CIF file as the structural model, instead of downloading from the PDB database.