Mesoscopic analysis of GABAergic marker expression in acetylcholine neurons in the whole mouse brain.

R. Oliver Goral, Snehashis Roy, Caroll A. Co, et al.


These are the instructions how to access the analyzed data which is made available through this platform. All files are accessible through open-source software, such as FIJI. Many files require a powerful computer to efficiently work with the data.


The data is organized by experimental group. All samples exist as duplicates due to the separation of left and right illumination sites.

Every sample folder contains these components:

- Folder "_masked": stiched down-sampled (2x2 or 3x3) image series with second partial brain hemisphere removed
- Folder "_FRST": image series of cell segmentation
- Folder "_FRST_seg": image series of cell segmentation results at various thresholds
- Folder "atlaslabel_": image series of registration to the Allen Brain Atlas v2

How to use:

Use "File>Import>Image Sequence...> and choose first file in the folder of interest
When prompted for further import parameters, choose "Virtual Stack" to reduce initial loading time

You can open several image sequences in parallel to compare different aspects of the post-processed dataset.
To ensure easy comparison, synchronize the image series using "Analyze>Tools>Synchronize Windows".
Check "Image scaling" in synchronization options for easy comparison between images.

Most images need to be adjusted for brightness and contrast to ensure visibility of image features.
This is achieved through "Image>Adjust>Brightness/Contrast" using the auto function.

Brain atlas registration images need to be re-colored to ensure color coding by brain region using "LUT>glasbey" or "LUT>glasbey_inverted".

For further questions or comments, contact rene.goral@nih.gov