Metadata file

The metadata file has information about each Patch-seq cell, including its different identifiers and assigned cell types.

File manifest

The file manifest contains URLs for the different data files associated with the Patch-seq cells that are located in various archives.

Transcriptomic data

Here, we have already downloaded the (large) transcriptomic expression data file. In that file, expression is quantified as counts-per-million (cpm), and each row is a gene and each column is a cell.

Let's create a 2D projection of the data using the transcriptomic data to see the structure of the different subclasses and types. We will transform the data, then use the UMAP algorithm to create a nonlinear embedding of a subset of the differentially expressed genes.

We can see where specific types fall in this embedding by using the metadata to identify specific cells.

We can also look at how expression of a particular gene varies across types in this embedding.

Finding cells with both electrophysiology and morphology data

All the cells in the public data set have both transcriptomic and electrophysiology data, but only some of them have morphological reconstructions.


Let's get the NWB file that has the electrophysiology data for this cell and use the IPFX library to process it.

We can also plot the particular sweep that we've been seeing the features of.


Now we'll get the SWC file that has the morphological reconstruction of this cell and use the neuron_morphology library to process it.

We can make a quick plot of the reconstruction.

Then we can calculate a set of morphological features.