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Merge pull request #16 from NeurodataWithoutBorders/port-tools
Add new tools documentation and update menu structure for analysis and acquisition tools
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‎archetypes/tools.md‎

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---
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title: "{{ replace .Name "-" " " | title }}"
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description: ""
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category: ""
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image: ""
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source_url: ""
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docs_url: ""
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weight: 100
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---
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## Description
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## Installation
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```bash
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# Installation command here
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```
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## Usage
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```python
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# Usage example here
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```
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## Additional Information

‎assets/css/style.css‎

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}
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.content li::marker {
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color: #d17128 !important;
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color: #374151 !important;
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}
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.content img[src$="#center"] {
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.contactP a {
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color: #171b26 !important;
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text-decoration: none !important;
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}
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}
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/* Tool Grid */
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.tool-grid {
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display: grid;
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grid-template-columns: repeat(auto-fill, minmax(300px, 1fr));
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gap: 2rem;
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margin: 2rem 0;
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}
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.tool-card {
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background: #fff;
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border: 1px solid #ebebeb;
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border-radius: 8px;
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overflow: hidden;
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transition: all 0.3s ease;
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height: 100%;
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}
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.tool-card:hover {
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box-shadow: 0 4px 6px -1px rgba(0, 0, 0, 0.1), 0 2px 4px -2px rgba(0, 0, 0, 0.1);
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transform: translateY(-2px);
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}
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.tool-image {
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height: 180px;
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overflow: hidden;
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display: flex;
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align-items: center;
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justify-content: center;
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background: #f5f5f5;
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}
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.tool-image img {
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max-width: 100%;
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max-height: 100%;
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object-fit: contain;
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padding: 1rem;
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}
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.tool-content {
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padding: 1.5rem;
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}
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.tool-content h3 {
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margin: 0 0 1rem 0;
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font-size: 1.25rem;
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}
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.tool-content p {
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margin: 0 0 1rem 0;
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color: #585c67;
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}
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.tool-links {
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display: flex;
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gap: 1rem;
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margin-top: 1rem;
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}
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.tool-links a {
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padding: 0.5rem 1rem;
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border-radius: 4px;
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text-decoration: none !important;
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font-weight: 500;
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font-size: 0.875rem;
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background-color: #114B7C;
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color: white !important;
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}
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.tool-links a:hover {
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opacity: 0.9;
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color: white !important;
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text-decoration: none !important;
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}
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@media (max-width: 768px) {
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.tool-grid {
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grid-template-columns: 1fr;
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}
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}

‎config/_default/menus.yaml‎

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weight: 1
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url: "nwb-software/"
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parent: "Software & Tools"
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- name: "NWB Tools"
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weight: 2
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url: "tools/"
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parent: "Software & Tools"
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- name: "Acquisition Tools"
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weight: 3
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url: "tools/acquisition/"
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parent: "Software & Tools"
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- name: "Analysis Tools"
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weight: 4
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url: "tools/analysis/"
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parent: "Software & Tools"
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# Community
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- name: "Community"

‎content/tools/_index.md‎

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---
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title: "NWB Tools"
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description: "A collection of tools for working with NWB data"
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---
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This page is a collection of tools we are cataloging as a convenience reference for NWB users. This is not a comprehensive list of NWB tools. Many of these tools are built and supported by other groups, and are in active development.
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## Tool Categories
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- [Acquisition and Control Tools]({{< ref "tools/acquisition" >}}) - Tools for data acquisition and experimental control
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- [Analysis and Visualization Tools]({{< ref "tools/analysis" >}}) - Tools for data analysis, visualization, and exploration
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**Disclaimer:** Reference herein to any specific product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not constitute or imply its endorsement, recommendation, or favoring by the NWB development team, United States Government or any agency thereof, or The Regents of the University of California. Use of the NeurodataWithoutBorders name for endorsements is prohibited.

‎content/tools/acquisition/_index.md‎

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---
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title: "Acquisition and Control Tools"
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description: "Tools for data acquisition and experimental control"
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---
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## Acquiring Electrophysiology Data
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{{< tool-grid category="electrophysiology" >}}
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## Controlling and Recording Behavioral Tasks
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{{< tool-grid category="behavior" >}}
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## Brain Data Modeling and Simulation
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{{< tool-grid category="modeling" >}}

‎content/tools/acquisition/arcontrol.md‎

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---
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title: "ArControl"
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description: "An Arduino based digital signals control system for animal behavioral platforms and Optogenetic TTL pulses, with tools for converting data to NWB format."
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category: "behavior"
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image: "/images/tools/arcontrol/arcontrol_logo.png"
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source_url: "https://github.com/chenxinfeng4/ArControl"
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weight: 40
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---
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## Description
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ArControl is an Arduino based digital signals control system. It is particularly useful for establishing animal behavioral platforms (like Skinner boxes), controlling devices to deliver stimulation, and monitoring behavioral responses. ArControl is also effective for generating Optogenetic TTL pulses.
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![ArControl Logo](/images/tools/arcontrol/arcontrol_logo.png)
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## Features
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- Arduino-based digital signal control
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- Behavioral platform control (e.g., Skinner box)
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- Stimulation delivery control
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- Behavioral response monitoring
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- Optogenetic TTL pulse generation
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## NWB Integration
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While ArControl does not currently support recording data directly in NWB format, it provides tools for converting ArControl data to NWB:
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- [NWB Conversion Tool](https://github.com/chenxinfeng4/ArControl-convert2-nwb)
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- [Conversion Demo Notebook](https://github.com/chenxinfeng4/ArControl-convert2-nwb/blob/main/playground/demo_convert.ipynb)
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## Resources
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- [Source Code](https://github.com/chenxinfeng4/ArControl)
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- [NWB Conversion Repository](https://github.com/chenxinfeng4/ArControl-convert2-nwb)

‎content/tools/acquisition/bmtk.md‎

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---
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title: "Brain Modeling Toolkit (BMTK)"
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description: "A suite for building and simulating network models at multiple levels of resolution, from biophysically-detailed, to point-neuron, to population-statistics approaches."
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category: "modeling"
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image: "/images/tools/bmtk/bmtk_levels_of_resolution_sm.png"
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source_url: "https://github.com/AllenInstitute/bmtk"
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docs_url: "https://alleninstitute.github.io/bmtk"
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weight: 50
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---
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## Description
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BMTK, SONATA, and Visual Neuronal Dynamics (VND) are mutually integrated software tools particularly suited to support large-scale bio-realistic brain modeling, but are applicable to a variety of neuronal modeling applications. BMTK is a suite for building and simulating network models at multiple levels of resolution, from biophysically-detailed, to point-neuron, to population-statistics approaches.
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![BMTK Levels of Resolution](/images/tools/bmtk/bmtk_levels_of_resolution_sm.png)
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## Features
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- Modular design for working across different scales of resolution
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- Support for different simulation engines with the same code interface
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- Integration with SONATA data format for:
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- Model architecture
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- Parameters
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- Simulation configuration
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- Input and output storage
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- Visualization through VND's rendering capabilities
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## NWB Integration
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BMTK provides support for NWB through its spike stimulus functionality. For more information, see the [NWB Spike Stimulus documentation](https://alleninstitute.github.io/bmtk/ecephys_probe.html).
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## Resources
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- [Documentation](https://alleninstitute.github.io/bmtk)
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- [Tutorials](https://alleninstitute.github.io/bmtk/tutorials.html)
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- [Source Code](https://github.com/AllenInstitute/bmtk)
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- [Publication](https://doi.org/10.1371/journal.pcbi.1008386)
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## Reference
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Dai et al. Brain Modeling Toolkit: An open-source software suite for multiscale modeling of brain circuits. PLoS Comput Biol 16(11): e1008386. https://doi.org/10.1371/journal.pcbi.1008386

‎content/tools/acquisition/mies.md‎

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---
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title: "MIES"
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description: "A sweep based data acquisition tool written in Igor Pro, featuring WaveBuilder for stimulus sets, DA_Ephys GUI for real-time control, and DataBrowser for data browsing."
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category: "electrophysiology"
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image: "/images/tools/mies/mies_screenshot.png"
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source_url: "https://github.com/AllenInstitute/MIES"
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docs_url: "https://alleninstitute.github.io/MIES/index.html"
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weight: 10
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---
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## Description
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MIES is a sweep based data acquisition tool written in Igor Pro. It provides three primary user interfaces designed to be operated in parallel.
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![MIES Screenshot](/images/tools/mies/mies_screenshot.png)
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## Primary Interfaces
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1. **WaveBuilder**
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- Generate stimulus sets
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2. **DA_Ephys GUI**
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- Control data acquisition in real time
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- Observe data during acquisition
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3. **DataBrowser**
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- Browse acquired data
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## NWB Integration
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MIES includes a dedicated [NWB Module](https://alleninstitute.github.io/MIES/IPNWB/index.html) for data export and integration.
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## Resources
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- [Documentation](https://alleninstitute.github.io/MIES/index.html)
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- [Video Tutorial](https://www.youtube.com/watch?v=Y3I-LDX-R2Q)
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- [NWB Module Documentation](https://alleninstitute.github.io/MIES/IPNWB/index.html)
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- [Source Code](https://github.com/AllenInstitute/MIES)

‎content/tools/acquisition/openephys.md‎

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---
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title: "Open Ephys GUI"
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description: "A modular, open-source software for extracellular electrophysiology, built by neuroscientists, with features for data acquisition, visualization, and extensibility through C++ modules."
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category: "electrophysiology"
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image: "/images/tools/openephys/openephys_gui_screenshot.png"
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source_url: "https://github.com/open-ephys/plugin-GUI"
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docs_url: "https://open-ephys.github.io/gui-docs/User-Manual/"
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weight: 20
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---
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## Description
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Open Ephys GUI is a modular, open-source software for extracellular electrophysiology. Built by neuroscientists, for neuroscientists, it provides all the features needed to acquire and visualize electrophysiology data, while making it easy to add new modules written in C++.
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![Open Ephys GUI Screenshot](/images/tools/openephys/openephys_gui_screenshot.png)
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## Features
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- Modular architecture for data acquisition and visualization
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- Configurable processing pipelines
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- Mix and match modules for custom workflows
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- Easy extension through C++ modules
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- Direct NWB format recording through plugin
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## NWB Integration
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Using the NWB format plugin, users can record data directly in NWB format via the OpenEphys GUI. The plugin provides seamless integration with the NWB ecosystem.
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### NWB Plugin Resources
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- [Plugin Documentation](https://open-ephys.github.io/gui-docs/User-Manual/Recording-data/NWB-format.html)
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- [Plugin Source Code](https://github.com/open-ephys-plugins/nwb-format)
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## Resources
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- [Website](https://open-ephys.org/gui)
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- [Documentation](https://open-ephys.github.io/gui-docs/User-Manual/)
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- [Source Code](https://github.com/open-ephys/plugin-GUI)

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