Tools

We’re focused on creating neuroanatomical models that can be used across neuroscience. This often entails developing approaches that enable data-driven analysis of brain organisation. In the following section, you’ll find descriptions and links to utilities and tools that we’ve developed.

BigBrainWarp. BigBrain is a singular dataset that offers an ultra-high-resolution (20µm) volumetric reconstruction of a sliced and stained post-mortem human brain (Amunts et al. 2013). BigBrainWarp aims to enable integration of BigBrain with neuroimaging and other neurobiological modalities, helping a wide range of neuroscientists to utilise the cytoarchitectural information encoded in BigBrain for multi-scale neuroscientific discovery. The toolbox is open and includes (i) histological features and pre-transformed maps in BigBrain and imaging spaces, (ii) codes for performing data transformations and (iii) extensive tutorials. Toolbox functions and tutorials are documented on readthedocs. We’ve updated and ported all the key tools from previous work into BigBrainWarp github.

Intracortical microstructure profiles. Depth-wise variations in image intensity can reveal architectonic differences across the cortex. We developed and validated a standardised procedure to generate microstructure profiles using either post mortem stained tissue or MRI. You can find the updated code in BigBrainWarp https://github.com/caseypaquola/BigBrainWarp/scripts/sample_intensity_profiles.sh.