Welcome to the repo for module 3. The demos/labs will be done within Jupyter Lab. To avoid all issues with compatibility and versions we recommend you to create and use a new conda environment. Download the environment.yml file and then run:
conda env create -f {path to the enviroment.yml file}
conda activate imaginganalysis
jupyter labextension install @jupyter-widgets/jupyterlab-manager ipyevents ipycanvas
jupyter labYou will need the datasets
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http://www.portugueslab.com/courses/LSMLSDA_2020/datasets/imaging.h5
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http://www.portugueslab.com/courses/LSMLSDA_2020/datasets/plane45.tif
Please download that data from: http://www.portugueslab.com/courses/LSMLSDA_2020/datasets/lightsheet_3D/imaging.h5
http://www.portugueslab.com/courses/LSMLSDA_2020/datasets/whole_brain/traces_better_deconvolved.h5
http://www.portugueslab.com/courses/LSMLSDA_2020/datasets/whole_brain/stimulus_log.h5
http://www.portugueslab.com/courses/LSMLSDA_2020/datasets/whole_brain/behavior_log.h5
http://www.portugueslab.com/courses/LSMLSDA_2020/datasets/whole_brain/coords.h5