Overview

Overview#

Welcome to the VASCilia documentation!

VASCilia: Vision Analysis StereoCilia#

A Napari Plugin for Deep Learning-Based 3D Analysis of Cochlear Hair Cell Stereocilia Bundles.

Pipeline Overview#

The following diagram illustrates the VASCilia pipeline for analyzing cochlear hair cell stereocilia bundles:

VASCilia pipeline diagram

Features#

VASCilia is a Napari plugin designed to facilitate 3D segmentation and quantification of stereocilia bundles in cochlear hair cells. Equipped with a variety of advanced features, VASCilia serves as a powerful tool for auditory research. Key functionalities include:

  • Open the Stack: Load and preprocess all frames in an image stack.

  • Upload Processed Stack: Import previously processed stacks using a pickle file.

  • Z-Focus Tracker: Automatically or manually select the cellular region of interest.

  • PCPAlignNet: Automatically or manually align and rotate stereocilia bundle rows to the planar cell polarity (PCP).

  • 3D BundleSeg: Perform 3D instance segmentation for the stereocilia bundles

  • Track and Visualize: Interactively visualize 3D stacks and segmentation results.

  • Bundle Deletion: Remove unnecessary regions from the analysis.

  • Tonotopic Region Prediction: Predict whether the analyzed region belongs to the BASE, MIDDLE, or APEX of the cochlea.

  • Cell Type Identification: Identify rows corresponding to IHC, OHC1, OHC2, and OHC3.

  • Measurement Analysis: Perform automatic 2D and 3D measurements with ease.

  • Fluorescence Intensity Analysis: Measure fluorescence intensity for any channel, generating a CSV file and plots for each cell type.

  • 3D Bundle Height Calculation: Calculate the length from the top of the bundle to its base.

  • Bundle Orientation: Obtain precise bundle orientation measurements.

  • Batch Processing: Enable high-throughput batch processing for multiple files.

  • Training Section: Allow other labs to fine-tune the model for their specific needs.

Applications#

VASCilia is particularly suited for:

  • Biomedical Cochlear Image Analysis: Analyze and interpret cochlear hair cell stereocilia bundles.

  • High-Throughput Processing: Streamline research studies with batch processing.

  • Quantitative Analysis: Conduct precise measurements of stereocilia bundles for auditory research.

Getting Started#

To get started with VASCilia: 1. Refer to the Installation section for setup instructions. 2. Check out the Quick Start: Demo Datasets and Tutorials guide for a simple example of using VASCilia.

For detailed instructions on specific features, refer to the Open Image and other feature pages.