CCFv3 Highlights: Getting Started

Getting started with CCF?

@maithamn has put together a Jupyter notebook tutorial as part of the Open for (Neuro)Science Symposium.

In the tutorial you will learn to:

  • Get started with the AllenSDK
  • Download and use the CCF average template. labels and structure graph
  • Analyze connectivity data using the CCF

You can also watch recording of the tutorial here.

Thanks a lot for the tutorial. I’m just getting started with the Allen Brain Atlas and the CCFv3 and this really helps! However, when executing the notebook, I’m encountering some bugs.

The first one is that the function imresize has been deprecated from scipy a while ago (and therefore the first cell doesn’t run). I managed to get rid of the problem by just deleting the import in the corresponding file of the package allensdk (the file being I guess downgrading scipy would also do the job and would be cleaner, but I need the last version for other purposes.

The second one is weirder: when executing the cell containing avg_temp, meta = mcc.get_template_volume(), I get the following error:
NRRDError: Size of the data does not equal the product of all the dimensions: 77045760-25821292=51224468
This is more a real problem as I’d really like to have the average template volume. Any idea why I get this error? I use the default resolution (25nm), and the corresponding shape of the annotated volume is (528, 320, 456).

Maybe that’s something really simple to solve but I confess I’m a complete newbie here. Thanks :slight_smile: