lyyu0926/mouse_brain_slam_imaging

Dataset Name: Mouse Brain SLAM (simultaneous label-free autofluorescence-multiharmonic microscopy) Images

This dataset contains multimodal microscopy imaging data, including 4-channel SLAM images, THG anisotropy data, and corresponding regional annotations/label maps.

📂 Data Hierarchy & Naming Convention

Each dataset folder follows the naming convention: [mouse model]_[orientation]_[age]_[acquisition date]

Folder Contents

For every acquisition, the following files are provided:

File Name	Description
dslam_4channel.tif	Raw Data: 4-channel SLAM image.
dslam_4channel.png	Preview: RGB visualization of the 4-channel SLAM data.
thg_polarization.tif	Raw Data: Third Harmonic Generation (THG) anisotropy/polarization image.
dslam_4channel_upsampled_label_map.npy	Annotation: High-resolution spatial label map (NumPy array).
dslam_4channel_upsampled_label_map.json	Metadata: Annotation parameters and label mapping information.
dslam_4channel_upsampled_label_map.png	Visual Reference: Color-coded version of the label map.

Regional Masks Subdirectory (/regional_masks)

Specific regions of interest (ROIs) are separated into individual mask files:

• region_mask_metadata.json: Metadata defining the regions and acquisition parameters.
• mask_[region_name].npy: Binary/categorical spatial data for a specific region.
• mask_[region_name].tif: High-bit depth image representation of the specific regional mask.

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🛠 Usage & Loading

Prerequisites