AMS-BP 0.4.0__tar.gz → 0.4.3__tar.gz

{ams_bp-0.4.0 → ams_bp-0.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.4.0
+Version: 0.4.3
 Summary: Advanced Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar
 Project-URL: Documentation, https://joemans3.github.io/AMS_BP/
 Project-URL: Source code, https://github.com/joemans3/AMS_BP
@@ -46,7 +46,7 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 
 > !!ATTENTION!! - Please note that you NEED to install the developmental dependencies to run the examples in full. This is mainly for installing the Jupyter notebook extensions, matplotlib and other visualization packages.
 
-[<img src="./docs/assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb)
+[<img src="./docs/assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](./examples/QuantitativeExperiments/PALM/fPALM/npc_palm.ipynb)
 
 [<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_widefield.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Widefield/widefield_twocolor.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_confocal.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Confocal/confocal_twocolor.ipynb)
 
@@ -63,31 +63,29 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 
 
 ### ***Installing the CLI tool using UV***
-
-
-
-
 1. [Install UV](https://docs.astral.sh/uv/getting-started/installation/).
 2. Run the command:
 ```bash
 uv tool install AMS_BP
 ```
-3. You will have access to two CLI commands (using the uv interface):
+3. You will have access to three CLI commands (using the uv interface):
     - `run_AMS_BP runsim` : This is the main entry point for the simulation. (see `run_AMS_BP runsim --help` for more details)
     - `run_AMS_BP config` : This is a helper tool to generate a template config file for the simulation. (see `run_AMS_BP config --help` for more details)
+    - `run_AMS_BP gui` : to start the GUI. See [GUI Documentation](./src/AMS_BP/gui/README.md)
     - Note: using `run_AMS_BP --help` will show you all the available commands.
 4. You can now use these tools (they are isolated in their own env created by uv, which is cool).
 
 ### ***PyPi***
 
-1. Run:
+1. If using pip, make sure the environment is python >= 3.12
+2. Run:
 ```bash
 pip install AMS_BP
 ```
 
 ## Command Line Interface
 
-AMS-BP provides a command-line interface with two main commands:
+AMS-BP provides a command-line interface with three main commands:
 
 ```bash
 # Generate a default configuration file
@@ -111,10 +109,10 @@ In addition to the CLI and programmatic API, AMS-BP comes with a graphical inter
 ### Main GUI Features
 The GUI provides the following tools from a single interface:
 
-**Create Configuration File** — Launches the visual configuration builder
-**Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
-**Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
-**Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
+- **Create Configuration File** — Launches the visual configuration builder
+- **Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
+- **Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
+- **Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
 
 ### Launch the GUI
 To start the GUI, run:
@@ -123,23 +121,7 @@ To start the GUI, run:
 
 run_AMS_BP gui
 ```
-#### Configuration Builder
-Clicking "Create Configuration File" opens a template selector where you can choose a preconfigured simulation (with preview images), and then visually edit all configuration options through dedicated tabs.
-
-Each section of the configuration is editable via structured UI forms, with contextual help and validation. Tabs include:
-
-- Global/Cell/Molecule/Condensate/Fluorophore parameters
-- Laser and optical configuration
-- Camera and channel settings
-- Experiment setup (e.g., z-stack vs time-series)
-Once ready, click "Preview Configuration TOML" to inspect the final file, and "Save" to export.
-
-#### Running Simulations from GUI
-Clicking "Run Simulation from Config" lets you select any .toml configuration file. A real-time log viewer shows progress, and outputs are saved in a structured AMS_runs/run_*/ directory.
-
-#### Sharing Logs
-Run into an issue? Use the packge logs button to select the logs corresponding to the simulation you just ran, save them and send them over to us! It will help you diagnose the issue!
-
+For detailed walkthrough see the [GUI Documentation](./src/AMS_BP/gui/README.md).
 ## Configuration File
 
 The configuration file (sim_config.toml) is divided into several key sections:

{ams_bp-0.4.0 → ams_bp-0.4.3}/README.md

@@ -20,7 +20,7 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 
 > !!ATTENTION!! - Please note that you NEED to install the developmental dependencies to run the examples in full. This is mainly for installing the Jupyter notebook extensions, matplotlib and other visualization packages.
 
-[<img src="./docs/assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb)
+[<img src="./docs/assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](./examples/QuantitativeExperiments/PALM/fPALM/npc_palm.ipynb)
 
 [<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_widefield.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Widefield/widefield_twocolor.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_confocal.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Confocal/confocal_twocolor.ipynb)
 
@@ -37,31 +37,29 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 
 
 ### ***Installing the CLI tool using UV***
-
-
-
-
 1. [Install UV](https://docs.astral.sh/uv/getting-started/installation/).
 2. Run the command:
 ```bash
 uv tool install AMS_BP
 ```
-3. You will have access to two CLI commands (using the uv interface):
+3. You will have access to three CLI commands (using the uv interface):
     - `run_AMS_BP runsim` : This is the main entry point for the simulation. (see `run_AMS_BP runsim --help` for more details)
     - `run_AMS_BP config` : This is a helper tool to generate a template config file for the simulation. (see `run_AMS_BP config --help` for more details)
+    - `run_AMS_BP gui` : to start the GUI. See [GUI Documentation](./src/AMS_BP/gui/README.md)
     - Note: using `run_AMS_BP --help` will show you all the available commands.
 4. You can now use these tools (they are isolated in their own env created by uv, which is cool).
 
 ### ***PyPi***
 
-1. Run:
+1. If using pip, make sure the environment is python >= 3.12
+2. Run:
 ```bash
 pip install AMS_BP
 ```
 
 ## Command Line Interface
 
-AMS-BP provides a command-line interface with two main commands:
+AMS-BP provides a command-line interface with three main commands:
 
 ```bash
 # Generate a default configuration file
@@ -85,10 +83,10 @@ In addition to the CLI and programmatic API, AMS-BP comes with a graphical inter
 ### Main GUI Features
 The GUI provides the following tools from a single interface:
 
-**Create Configuration File** — Launches the visual configuration builder
-**Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
-**Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
-**Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
+- **Create Configuration File** — Launches the visual configuration builder
+- **Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
+- **Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
+- **Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
 
 ### Launch the GUI
 To start the GUI, run:
@@ -97,23 +95,7 @@ To start the GUI, run:
 
 run_AMS_BP gui
 ```
-#### Configuration Builder
-Clicking "Create Configuration File" opens a template selector where you can choose a preconfigured simulation (with preview images), and then visually edit all configuration options through dedicated tabs.
-
-Each section of the configuration is editable via structured UI forms, with contextual help and validation. Tabs include:
-
-- Global/Cell/Molecule/Condensate/Fluorophore parameters
-- Laser and optical configuration
-- Camera and channel settings
-- Experiment setup (e.g., z-stack vs time-series)
-Once ready, click "Preview Configuration TOML" to inspect the final file, and "Save" to export.
-
-#### Running Simulations from GUI
-Clicking "Run Simulation from Config" lets you select any .toml configuration file. A real-time log viewer shows progress, and outputs are saved in a structured AMS_runs/run_*/ directory.
-
-#### Sharing Logs
-Run into an issue? Use the packge logs button to select the logs corresponding to the simulation you just ran, save them and send them over to us! It will help you diagnose the issue!
-
+For detailed walkthrough see the [GUI Documentation](./src/AMS_BP/gui/README.md).
 ## Configuration File
 
 The configuration file (sim_config.toml) is divided into several key sections:

{ams_bp-0.4.0 → ams_bp-0.4.3}/docs/index.md

@@ -1,15 +1,34 @@
-# AMS-BP User Guide
+# AMS-BP
 <p>
-<img src="assets/icons/drawing.svg" alt="AMS-BP Logo" width="500" height="200">
+<img src="./assets/icons/drawing.svg" alt="AMS-BP Logo" width="500" height="200">
 </p>
+
 ## Advanced Fluorescence Microscopy Simulation Tool
 
 AMS-BP is a powerful simulation tool for advanced fluorescence microscopy experiments. This guide covers both command-line usage and library integration.
 
+## Overview of Simulation Workflow
+<img align = "left" src="./assets/figures/Fig1_Schema.svg" width="500"/>
+
+*A ground truth is created, **a**, with $`f_{n}`$ fluorophore types of $`N_{f_{n}}`$ molecules each. If applicable, the motion of these molecules is modelled using a 3D bounded FBM with fluctuating generalized diffusion coefficients and Hurst parameters. Variations are modelled as a Markov Chain and require rate constants as parameters. Different fluorophores can have different motion models. The resolution of the motion models is $`\Delta t`$ and cannot be smaller than 1 ms (for computational efficiency). Given the microscope parameters specific to the experimental procedure to simulate, at every time $`t_{j}`$, the excitation intensity for each channel (**b**) is calculated at each fluorophore's location, **c**. For $`t_{j} \rightarrow t_{j+\Delta t}`$, the photophysical state trajectory of the fluorophore is simulated using the light intensity at the molecule's location as input for any light-dependent transition rates, **d**. For the duration that the shutter is open and light is emitted from the sample, emission filters for each channel are applied before the convolution with PSF models, **e**. The incident photons on the detector are then converted to photoelectrons and finally to digital units using the detector models provided, **f**.*
+
+## API Reference and Docs
+Find detailed API references for the library at: [joemans3/github.io/AMS_BP](https://joemans3.github.io/AMS_BP/)
+> A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](../examples/VisualizingIndividualModules/modules_explained.ipynb). Then head over to the [laser modulation module](../examples/VisualizingIndividualModules/laser_modulation.ipynb) which will show how to change the laser power over time in the simulations. Then view an example of a complex experiment setup for [FRAP](../examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
+
+## Examples (Click on the image buttons to be taken to the Jupyter notebooks):
+
+> !!ATTENTION!! - Please note that you NEED to install the developmental dependencies to run the examples in full. This is mainly for installing the Jupyter notebook extensions, matplotlib and other visualization packages.
+
+[<img src="./assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](../examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](../examples/QuantitativeExperiments/PALM/fPALM/npc_palm.ipynb)
+
+[<img src="./assets/buttons/ButtonFigure_zstack_twocolor_widefield.svg" width="300"/>](../examples/QuantitativeExperiments/TwoColor/Widefield/widefield_twocolor.ipynb) [<img src="./assets/buttons/ButtonFigure_zstack_twocolor_confocal.svg" width="300"/>](../examples/QuantitativeExperiments/TwoColor/Confocal/confocal_twocolor.ipynb)
 
+[<img align="middle" src="./assets/buttons/ButtonFigure_sptPALM_mmaple.svg" width="300"/>](../examples/QuantitativeExperiments/PALM/sptPALM/motionmodels_sptmmaple.ipynb)
 ## Table of Contents
-- [Installation](#installation) 
+- [Installation](#installation)
 - [Command Line Interface](#command-line-interface)
+- [GUI](#gui)
 - [Configuration File](#configuration-file)
 - [Running Experiments](#running-experiments)
 - [Advanced Usage](#advanced-usage)
@@ -18,23 +37,29 @@ AMS-BP is a powerful simulation tool for advanced fluorescence microscopy experi
 
 
 ### ***Installing the CLI tool using UV***
-
-
-
-
 1. [Install UV](https://docs.astral.sh/uv/getting-started/installation/).
 2. Run the command:
 ```bash
 uv tool install AMS_BP
 ```
-3. You will have access to two CLI commands (using the uv interface):
+3. You will have access to three CLI commands (using the uv interface):
     - `run_AMS_BP runsim` : This is the main entry point for the simulation. (see `run_AMS_BP runsim --help` for more details)
     - `run_AMS_BP config` : This is a helper tool to generate a template config file for the simulation. (see `run_AMS_BP config --help` for more details)
+    - `run_AMS_BP gui` : to start the GUI. See [GUI Documentation](../src/AMS_BP/gui/README.md)
     - Note: using `run_AMS_BP --help` will show you all the available commands.
 4. You can now use these tools (they are isolated in their own env created by uv, which is cool).
+
+### ***PyPi***
+
+1. If using pip, make sure the environment is python >= 3.12
+2. Run:
+```bash
+pip install AMS_BP
+```
+
 ## Command Line Interface
 
-AMS-BP provides a command-line interface with two main commands:
+AMS-BP provides a command-line interface with three main commands:
 
 ```bash
 # Generate a default configuration file
@@ -42,6 +67,9 @@ run_AMS_BP config [OPTIONS]
 
 # Run a simulation using a configuration file
 run_AMS_BP runsim CONFIG_FILE
+
+#start the GUI
+run_AMS_BP gui
 ```
 
 ### Config Command Options
@@ -49,17 +77,30 @@ run_AMS_BP runsim CONFIG_FILE
 - `-o, --output_path PATH`: Specify the output directory for the configuration file
 - `-r, --recursive_o`: Create output directory if it doesn't exist
 
+## GUI
+In addition to the CLI and programmatic API, AMS-BP comes with a graphical interface to guide users through the configuration, simulation, and analysis pipeline.
 
-## Overview of Simulation Workflow
-![Overview Schematic](./assets/figures/Fig1_Schema.svg)
-*A ground truth is created, **a**, with $`f_{n}`$ fluorophore types of $`N_{f_{n}}`$ molecules each. If applicable, the motion of these molecules is modelled using a 3D bounded FBM with fluctuating generalized diffusion coefficients and Hurst parameters. Variations are modelled as a Markov Chain and require rate constants as parameters. Different fluorophores can have different motion models. The resolution of the motion models is $`\Delta t`$ and cannot be smaller than 1 ms (for computational efficiency). Given the microscope parameters specific to the experimental procedure to simulate, at every time $`t_{j}`$, the excitation intensity for each channel (**b**) is calculated at each fluorophore's location, **c**. For $`t_{j} \rightarrow t_{j+\Delta t}`$, the photophysical state trajectory of the fluorophore is simulated using the light intensity at the molecule's location as input for any light-dependent transition rates, **d**. For the duration that the shutter is open and light is emitted from the sample, emission filters for each channel are applied before the convolution with PSF models, **e**. The incident photons on the detector are then converted to photoelectrons and finally to digital units using the detector models provided, **f**.*
+### Main GUI Features
+The GUI provides the following tools from a single interface:
+
+- **Create Configuration File** — Launches the visual configuration builder
+- **Run Simulation from Config** — Select a .toml file and run the simulation with logging and progress tracking
+- **Visualize Microscopy Data (Napari)** — Open TIFF, PNG, ND2, or Zarr image files and view with the Napari viewer
+- **Package Logs for Sharing** — Package run directories (e.g., run_2024_04_20_001) into a .zip file for archival or collaboration
 
+### Launch the GUI
+To start the GUI, run:
 
+```bash
+
+run_AMS_BP gui
+```
+For detailed walkthrough see the [GUI Documentation](../src/AMS_BP/gui/README.md).
 ## Configuration File
 
 The configuration file (sim_config.toml) is divided into several key sections:
 
-#### For a detailed description of the configuration file, refer to the [Configuration File Reference](./API_Documentation/sim_config.md).
+#### For a detailed description of the configuration file, refer to the [Configuration File Reference](https://joemans3.github.io/AMS_BP/API_Documentation/sim_config/).
 ### Basic Units
 ```toml
 version = "0.1"
@@ -99,7 +140,8 @@ diffusion_unit = "um^2/s" # diffusion coefficient units
 
 ## Running Experiments
 
-AMS-BP supports two types of experiments:
+AMS-BP's CLI currently supports two types of experiments:
+> (however this can be extended when used as a library) 
 
 ### 1. Time Series
 ```toml
@@ -120,39 +162,25 @@ laser_names_active = ["red", "blue"]
 laser_powers_active = [0.5, 0.05]
 laser_positions_active = [[5, 5, 0], [5, 5, 0]]
 ```
-
-## Advanced Usage
-
-### Using AMS-BP as a Library
-
-For programmatic control, you can import and use AMS-BP as a Python library:
-
-```python
-from AMS_BP.configio.convertconfig import ConfigLoader
-
-# Configuration loader intialization
-config_loader = ConfigLoader(config_path="path/to/config.toml")
-
-# Setup microscope
-setup_config = config_loader.setup_microscope()
-microscope = setup_config["microscope"]
-config_exp = setup_config["experiment_config"]
-function_exp = setup_config["experiment_func"]
-
-# Run simulation
-frames, metadata = function_exp(microscope=microscope, config=config_exp)
-
-# Save results
-from AMS_BP.configio.saving import save_config_frames
-save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
+To run the default configuration:
+1. Make sure you followed the uv tool installation.
+2. Make a copy of the default configuration file using the command:
+```bash
+run_AMS_BP config
 ```
+3. Run the sim:
+```bash
+run_AMS_BP runsim sim_config.toml
+```
+4. View the results in the newly created folder, whose name is defined in the config file.
 
-### Key Components When Using as Library
-
-1. **ConfigLoader**: Handles configuration file parsing and validation
-2. **Microscope**: Represents the virtual microscope setup
-3. **Experiment Functions**: Control experiment execution
-4. **Save Functions**: Handle data output
+## High Priority Features
+~~1. Irregular cell shapes with motion models~~ (supported with release of v0.2.0)
+2. Stimulated Emission models
+3. STORM workflow examples
+4. CTRW motion models
+5. Simpler configurations
+> **_NOTE:_** Please note that this application DOES NOT currently model the process of stimulated emission, and as such is not suitable for simulating stimulated emission microscopy ([STED](https://en.wikipedia.org/wiki/STED_microscopy))-type experiments. Work in this area is ongoing.
 
 ### Custom Experiment Types
 
@@ -163,18 +191,6 @@ When using AMS-BP as a library, you can create custom experiment types by:
 3. Defining new molecule behaviors
 4. Creating specialized analysis routines
 
-## API Reference and Docs
-Find detailed API references for the library at: [joemans3/github.io/AMS_BP](https://joemans3.github.io/AMS_BP/)
-> A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](examples/VisualizingIndividualModules/modules_explained.ipynb). Then head over to the [laser modulation module](examples/VisualizingIndividualModules/laser_modulation.ipynb) which will show how to change the laser power over time in the simulations. Then view an example of a complex experiment setup for [FRAP](examples/QuantitativeExperiments/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
-
-## High Priority Features
-1. Irregular cell shapes with motion models
-2. Stimulated Emission models
-3. STORM workflow examples
-4. CTRW motion models
-5. Simpler configurations
-
-
 ## Tips and Best Practices
 
 1. **Configuration Management**

{ams_bp-0.4.0 → ams_bp-0.4.3}/src/AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.4.0"
+__version__ = "0.4.3"

ams_bp-0.4.3/src/AMS_BP/gui/README.md

@@ -0,0 +1,81 @@
+# AMS-BP GUI
+
+The AMS-BP GUI provides a user-friendly interface for constructing and validating configuration files for the AMS-BP fluorescence microscopy simulation framework. It integrates simulation execution, configuration design, log packaging, and data visualization in one cohesive window.
+
+## Overview
+
+This GUI supports:
+
+- A template-based configuration builder for quick setup.
+- A visual editor for each simulation parameter block (cells, molecules, fluorophores, lasers, etc.).
+- Interactive help sections for each tab.
+- Simulation execution using prebuilt configs.
+- Napari integration for visualization of resulting microscopy data.
+- Packaging of simulation logs for easy sharing.
+
+## Launching the GUI
+
+```bash
+run_AMS_BP gui
+```
+## GUI Structure
+
+### Main Window
+The main window (MainWindow) acts as the launchpad for:
+
+- Configuration Builder — Launches a template selector and opens a full editor.
+- Run Simulation from Config — Lets you pick a .toml file and start the simulation.
+- Visualize Microscopy Data — Opens TIFF and other images in a Napari viewer.
+- Package Logs for Sharing — Archives a run_* folder into a .zip.
+
+#### Configuration Editor
+Once a template is selected, the ConfigEditor is launched. It contains:
+
+- A dropdown navigation system replacing traditional tabs.
+- A floating tab counter and preview/save buttons.
+- A help button per section (reads *.md files from help_docs/).
+- Live validation using internal config models (convertconfig.py).
+
+##### Tabs & Widgets
+Each configuration section is implemented as a modular PyQt widget, including:
+
+- GlobalConfigWidget
+- CellConfigWidget
+- MoleculeConfigWidget
+- FluorophoreConfigWidget
+- CondensateConfigWidget
+- LaserConfigWidget
+- ExperimentConfigWidget
+- ...and more
+
+Each widget supports:
+
+- get_data() → Extract validated dictionary data
+- set_data(data: dict) → Load existing config into the UI
+- validate() → Validate using backend logic
+- get_help_path() → Load the corresponding markdown help page
+
+####  Running a Simulation
+
+Once you've completed the config file setup via the GUI:
+
+- Click "Preview Configuration TOML" to confirm contents.
+- Click "Ready to Save Configuration" and choose a .toml path.
+- Return to the main window, click "Run Simulation from Config".
+- Simulation will launch in a background thread and print logs to a live window.
+- Once done, results will be saved in a run_*/ folder.
+
+#### Viewing Results
+
+- Click "Visualize Microscopy Data (Napari)"
+- Select any .tif, .tiff, .nd2, or .zarr file
+
+The data will be loaded into a new Napari viewer session
+
+#### Packaging Logs
+
+To share or archive a completed simulation:
+
+- Click "Package Logs for Sharing".
+- Select the run_* folder you want.
+- Choose a destination for the .zip file.