freesia_4.0_C1_488nm_10X.json

qianqianyuan1997 commented 4 months ago

i want to know details in this file

WPQ-ZH commented 4 months ago

I would also like to ask what files should be prepared when using NEATMAP, the test data set provided by the author is downloaded and decompressed always shows corruption

ZWJ-tech commented 4 months ago

Hi, @WPQ-ZH

Data availability：https://zenodo.org/records/8133486

NEATmap requires continuous whole-brain section data in TIFF format and provides file information (such as freesia_4.0_C3_488nm_10X.json in the downloaded test data). After downloading the files from the data availability (BrianImage_group.zip.001-007), you select all the files and extract them together. Extracting the files in this manner prevents errors.

ZWJ-tech commented 4 months ago

Hi, @qianqianyuan1997

The test data includes freesia_4.0_C3_488nm_10X.json. Using NEATmap requires correctly specifying the input channel number.

The freesia_4.0_C3_488nm_10X.json contains information about each image of the whole brain, including:

group_size: 75, meaning every 75 images (voxel size of 4x4x4 $μm^3$) form a 300-micrometer thick brain section.
image_path: 4.0, indicating the relative path to the whole brain data.
index, height, width, file_name: These pieces of information, along with the aforementioned details, are used in NEATmap to load the data.

mesobrain / NEATmap_software

freesia_4.0_C1_488nm_10X.json #3