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Viewing Manual Markings
MATLAB is required for viewing our markings. All scripts have been validated on a Windows 10 system running MATLAB 2017b. Note that MATLAB2017b or higher is required.
Users can access the original recordings from the following links:
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Allen Brain Observatory: Please follow the instructions at Allen Institute's GitHub page. Recordings are located in the visual-coding-2p → ophys_movies folder of the S3 bucket and are titled as “ophys_experiment_X.h5”, where X is the experiment ID reported in our manuscript.
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Neurofinder: Recordings from this challenge can be downloaded from the Neurofinder's GitHub repository Note that we have manually marked the 01, 02, and 04 datasets. Note that with the provided markings, cropped videos are requires. If you have the original recordings from the above links, place them in their corresponding folders in the Dataset folder. For the Neurofinder challenge, data files downloaded from the website should be placed in Dataset→Neurofinder folder and named as, for example, neurofinder.01.00.test and neurofinder.01.00 for test and train data, respectively. Each folder should contain the “images” folder that consists of the .tiff images of the recording.
Open the view_marking.m script in MATLAB. Please follow the instructions written in this script to set the correct parameters. Run the script after parameters are set.
This script will open two GUI windows. In the first GUI, you will view all the markings overlaid on the full field-of-view recording. In the second GUI, you can navigate through each neuron’s masks and traces.
** This script will take a while to read and prepare the data for visualization.