This contains the scripts used to extract traces from GCaMP movies contained in the NeuroPAL publication, "NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans". The publication is available here: https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2

The NeuroPAL ID software, used in conjunction with these scripts, is available here: https://github.com/amin-nejat/CELL_ID

Simply add information about where input data is located in src/analyze.m.

• id_run: the _ID.mat file generated using the NeuroPAL ID software.
• gcamp_run: An nd2 file that contains a 2D image time series of volumes obtained by sweeping through z.

The remainder of analyze.m has the workflow:

1. preprocess_video.m: The 2D time series will be converted to a 3D time series that is slightly filtered and compressed.
2. get_ID_annotations.m: Data from the ID run (including annotations of neurons) is ingested and matched to the first frame.
3. get_traces.m: Neurons are tracked throughout the time series, and calcium values are extracted.

The output of this script is an traces.mat file containing the following: input_neurons = the neurons ID'd in the _ID.mat file, generated using the NeuroPAL ID software. positions = an array of neuron positions (x,y,z), per video frame, corresponding to the input_neurons array. trace_array = an array of GCaMP intensities, per video frame, corresponding to the input_neurons array. times = the real time per video frame.

For further information please contact the corresponding authors.