> For the complete documentation index, see [llms.txt](https://bakingtray.mouse.vision/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://bakingtray.mouse.vision/developers/gallery.md).

# Gallery

## Rat brain with sparse labelling

A rat brain labelled with eGFP via a systemic viral injection. Data from Viktor Plattner.

![](https://3832012848-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MAVhQ1tbEzz1UZd9NDb%2Fuploads%2Fgit-blob-a501bcbf35bd55e477822a82abad998697af4f33%2Frat_3d.jpg?alt=media)

## Seamless 3-D volumes

The following panels show a transgenic mouse brain expressing tdTomato (yellow) in somatostatin neurons. The brain was cut in the coronal plane and shows seamless reslices in the horizontal and sagittal planes. Single axons are clearly visible in the detailed views.

![](https://3832012848-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MAVhQ1tbEzz1UZd9NDb%2Fuploads%2Fgit-blob-2283ae2b511b8e1543962c7619d9fca9b17ccbb6%2Fsst_gallery.jpg?alt=media)

This is a movie of a mouse brain which was injected with a GFP viral tracer. The the grey shows background fluorescence.

{% embed url="<https://www.youtube.com/watch?v=NaDrk2N9iBg>" %}

## RGB imaging

The following movie was obtained using tdTomato, GGP, and BFP. Sample imaged at 790 nm using a 2-photon laser. Sections taken every 25 microns. Artifacts arise from the very thin sections that sometimes float between the sample and the objective.

{% embed url="<https://youtu.be/cLhQb5BEKjQ>" %}

![Representative slices extracted from the above data. These images have a highlighted border added and the damage shown in the movie was digitally removed.](https://3832012848-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MAVhQ1tbEzz1UZd9NDb%2Fuploads%2Fgit-blob-074673046e0ef3731a025b029eb9d277b90800fd%2FAzimuthInjectionCollage_3color.jpg?alt=media)

![Higher resolution detail from one of the above slices.](https://3832012848-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MAVhQ1tbEzz1UZd9NDb%2Fuploads%2Fgit-blob-4044d3122cb90c86012b534346ec47c6a6091a75%2FAzimuthInjection_choiceImage_crop_corner.jpg?alt=media)

## Tracing neurites from single cells

Moving showing single cortical neurons expressing GFP after plasmid electroporation.

{% embed url="<https://youtu.be/vBPPI2r1B1E>" %}

## Pulvinar neurons projecting to cortical area AL

These maximum intensity projections come from data generated by Ioana Gasler. They are RetroAAV cre in AL and flex mCherry in the pulvinar. Data were acquired at 2.2 x 2.2 x 10 µm. Images are max intensity projections of the full volume along different axes, with a bit of Gaussian blur for smoothing (sigma = 1 µm). The volume shown is roughly 4.7 x 3.6 x 6.0 mm (ML x DV x AP). Note that despite the relatively large step size (10 µm) between optical planes, it is easy to follow the single axons.

![Pixel size is 2.2 by 2.2 microns and data are a max intensity projection over a small number of planes.](https://3832012848-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MAVhQ1tbEzz1UZd9NDb%2Fuploads%2Fgit-blob-30f6285ac67cdc07edb95dd1641f1d44fe2fe7ec%2FTC_cell_coronal.jpg?alt=media)

![Pixel size along rows is 2.2 microns but along columns is 10 microns. Data are a max intensity projection over a small number of planes.](https://3832012848-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MAVhQ1tbEzz1UZd9NDb%2Fuploads%2Fgit-blob-823b384fc881b229da70fa9458853eaa49ab43d4%2FTC_cell_transverse.jpg?alt=media)

![Pixel size along rows is 10 microns but along columns is 2.2 microns. Data are a max intensity projection over a small number of planes.](https://3832012848-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MAVhQ1tbEzz1UZd9NDb%2Fuploads%2Fgit-blob-ddc684ced1848d314d57069c6409f5d37b07d29f%2FTC_cells_sagittal.jpg?alt=media)