How to start processing the raw imaging data generated with a Miniscope, including developing a usable pipeline and demoing the Minion pipeline.

The direction of miniature microscopes, including both MetaCell and other groups.

Overview of the content for Day 2 of this course.

Summary and closing remarks for this three-day course.

This hands-on tutorial explains how to run your own Minion session in the MetaCell cloud using jupityr notebooks.

In this hands-on analysis tutorial, users will mimic a kernel crash and learn the steps to restore inputs in such a case.

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

This final hands-on analysis tutorial walks users through the last visualization steps in the cellular data.

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

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. 

In this hands-on session, you will learn how to explore and work with DataLad datasets, containers, and structures using Jupyter notebooks. 

This talk covers the differences between applying HED annotation to fMRI datasets versus other neuroimaging practices, and also introduces an analysis pipeline using HED tags. 

This lesson provides a thorough description of neuroimaging development over time, both conceptually and technologically. You will learn about the fundamentals of imaging techniques such as MRI and PET, as well as how the resultant data may be used to generate novel data visualization schemas. 

This video shows how to use the brainlife.io interface to edit the participants' info file. This file is the ParticipantInfo.json file of the Brain Imaging Data Structure (BIDS).

This quick video presents some of the various visualizers available on brainlife.io

This video demonstrates each required step for preprocessing T1w anatomical data in brainlife.io.

Longitudinal Online Research and Imaging System (LORIS) is a web-based data and project management software for neuroimaging research studies. It is an open source framework for storing and processing behavioural, clinical, neuroimaging and genetic data. LORIS also makes it easy to manage large datasets acquired over time in a longitudinal study, or at different locations in a large multi-site study.

This talk covers the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC), a free one-stop-shop collaboratory for science researchers that need resources such as neuroimaging analysis software, publicly available data sets, or computing power.

This lecture provides an introduction to reproducibility issues within the fields of neuroimaging and fMRI, as well as an overview of tools and resources being developed to alleviate the problem.