Accessing raw images from patch-seq morphological reconstructions

How To
1

Hi I’m interested in looking more closely at some of the morphologies of the cells in from the Gouwens et al 2020 patch-seq dataset. I’ve been about to download and visualize the reconstructed morphologies but I was also hoping to look at the raw data. I’m looking for axonal varicosities but the detail of the reconstruction understandably doesn’t seem to be that precise.

Any help would greatly appreciated!

2

Just bumping this to see if anyone can provide some help

3

Hello @jratliff thanks for your interst in our data. Although our patch-clamp/seq slices are not specifically tailored for capturing ultrastructure details, I have included links below to patch-clamp stacks for both mouse and human samples. Feel free to assess whether they meet your requirements. Once you open the link, click on “view image stack” to access the single-plane image viewer.

Mouse

Human

4

Thanks for this! I didn’t see that this portal had some of the same crosses from the paper. Is there overlap between these two in terms of specific cells? For instance could I search for a specimen ID from the Gouwens et al collection: Brain Knowledge Platform. In the cell feature search database?

5

Hello, they are not overlaping datasets. Most neurons within the Allen Cell Types Database are from patch-clamp experiments and not patch-seq. However, I think it is still a good tool to assess whether the image stacks will meet your requirements.