3D fluorescence dataset of tissue cleared pig cochlea
Data files
Jun 04, 2025 version files 26.53 GB
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6-8w-pig-cochlea-TuJ1.zip.001
8.52 GB
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6-8w-pig-cochlea-TuJ1.zip.002
8.52 GB
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6-8w-pig-cochlea-TuJ1.zip.003
8.52 GB
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6-8w-pig-cochlea-TuJ1.zip.004
959.29 MB
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README.md
1.46 KB
Abstract
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.
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 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. The first level of 5 folders, named as YYYYYY (6 digits), contains a row of tiles. The second level of 5 folders, named as YYYYYY_XXXXXX (6 + 6 digits), contains a stack of images which share the same x and y coordinates. Each stack contains 291 images at different z locations, named as YYYYYY_XXXXXX_ZZZZZZ (6 + 6 + 6 digits). In total, there are 5 × 5 × 291 tiff files.
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.