3D fluorescence dataset of tissue cleared pig cochlea

Tissue clearing and light-sheet fluorescence microscopy were applied for 3D profiling of intact cochleae. However, the spiral ganglion neurons (SGNs) remain relatively understudied compared to hair cells and supporting cells, especially in large animal models. Here we: 1) introduced collagenase treatment to the current protocol of tissue clearing to enhance uniform antibody staining of SGNs within the pig cochlea, and 2) adopted a deep learning object detection model to locate and count SGNs in large 3D datasets via Spiner (Spiral ganglion neuron profiler). This is an example pig cochlea dataset for running the designed Spiner workflow. The dataset is structured by TeraStitcher compatible two-level hierarchy of folders, and the TIFF images can be opened with image tools (e.g., ImageJ) that support the TIFF format. ,
A cochlea from a wild-type 6-8-week-old Yorkshire pig was cleared and stained using a modified BoneClear protocol. The cleared pig cochlea was imaged using a custom-built light sheet fluorescence microscope by illumination of 640 nm (anti-TuJ1, AF647), with a voxel size of 0.65 × 0.65 × 10 μm3. 
, # 3D fluorescence dataset of tissue cleared pig cochlea

## 6-8w-pig-cochlea-TuJ1

3D fluorescence image dataset of a tissue cleared pig cochlea of a 6-8-week-old wildtype Yorkshire pig, with TuJ1 labeling of spiral ganglion neurons.

## Description of the data and file structure

This is an example dataset for running the [Spiner](https://doi.org/10.5281/zenodo.15273059) workflow.
The dataset contains tiff images which can be opened with image tools (e.g., ImageJ) that support tiff format. Each tiff file, if not empty, is a fluorescence image (2048 × 2048) of the pig cochlea at certain location.
The 3D dataset was acquired using a custom-built light sheet fluorescence microscope by illumination of 640 nm, with a voxel size of 0.65 × 0.65 × 10 μm^3. The corresponding staining information is shown below.

| Primary | Secondary |
| :-------: | :-------: |
| anti-TuJ1 | AF647 |

The files were structured by [TeraStitcher compatible two-level hierarchy of folders](https://github.com/a...,