Overview of Day 2 of this course.

"Faster & more sensitive imaging with the MiniFAST" was presented by Caleb Kemere at the 2021 Virtual Miniscope Workshop as part of a series of talks by leading Miniscope users and developers.

Running your own Minion session in the MetaCell cloud using jupityr notebooks

Mimicking a kernel crash, and walking through the steps to restore your inputs.

This lesson will go through how to extract cells from video that has been cleaned of background noise and motion.

Visualizing the final results

This lecture covers infrared LED oblique illumination for studying neuronal circuits in in vitro block-preparations of the spinal cord and brain stem.

This lecture provides an introduction to the study of eye-tracking in humans. 

This lecture covers the application of diffusion MRI for clinical and preclinical studies.

This lecture provides an introduction to the application of genetic testing in neurodevelopmental disorders.

This lesson contains both a lecture and a tutorial component. The lecture (0:00-20:03 of YouTube video) discusses both the need for intersectional approaches in healthcare as well as the impact of neglecting intersectionality in patient populations. The lecture is followed by a practical tutorial in both Python and R on how to assess intersectional bias in datasets. Links to relevant code and data are found below. 

This tutorial walks participants through the application of dynamic causal modelling (DCM) to fMRI data using MATLAB. Participants are also shown various forms of DCM, how to generate and specify different models, and how to fit them to simulated neural and BOLD data.

This lesson corresponds to slides 158-187 of the PDF below. 

Tutorial describing the basic search and navigation features of the Allen Mouse Brain Atlas

Tutorial describing the basic search and navigation features of the Allen Developing Mouse Brain Atlas

This tutorial demonstrates how to use the differential search feature of the Allen Mouse Brain Atlas to find gene markers for different regions of the brain and to visualize this gene expression in three-dimensional space. Differential search is also available for the Allen Developing Mouse Brain Atlas and the Allen Human Brain Atlas.

Research Resource Identifiers (RRIDs) are ID numbers assigned to help researchers cite key resources (antibodies, model organisms and software projects) in the biomedical literature to improve transparency of research methods.

GeneWeaver is a web application for the integrated cross-species analysis of functional genomics data to find convergent evidence from heterogeneous sources. The application consists of a large database of gene sets curated from multiple public data resources and curated submissions, along with a suite of analysis tools designed to allow flexible, customized workflows through web-based interactive analysis or scripted API driven analysis. Gene sets come from multiple widely studied species and include ontology annotations, brain gene expression atlases, systems genetic study results, gene regulatory information, pathway databases, drug interaction databases and many other sources. Users can retrieve, store, analyze and share gene sets through a graded access system. Analysis tools are based on combinatorics and statistical methods for comparing, contrasting and classifying gene sets based on their members.

This tutorial shows how to use the UCSC genome browser to find a list of genes in a given genomic region.

This tutorial shows how to find all the single nucleotide polymorphisms upstream from genes using the UCSC Genome Browser.

This tutorial demonstrates how to find all the single nucleotide polymorphisms in a gene using the UCSC Genome Browser.