ImageSeries

Storage of ImageSeries

Use external mode for videos of animals

When storing videos of natural behavior using the ImageSeries the file should be stored as an external file. That is, the file should be packaged together with the nwb file instead of stored inside the format. This can be accomplished by using the external_file file option to store the path instead. This is preferred for videos because it allows the usage of video compression codecs that are lossy and highly optimized for such videos.

Check function: check_image_series_data_size()

Use internal dataset for videos of neurophysiological data

When storing a TwoPhotonSeries or other videos of neural data, lossy compression should not be used, and it is best to store the this data within a Dataset in the NWB file and use chunking and lossless compression to reduce the disk space.

Use relative path for external mode

When using external_file the paths passed in the external_file option should be relative to the location of the nwb file.

Check function: check_image_series_external_file_relative()

Starting frame only with external file

The starting_frame attribute of an ImageSeries is only relevant when using external files. If there is no external file, there should be no starting frame set. This is a legacy issue that was possible in older versions of PyNWB (< 2.2.0).

Check function: check_image_series_starting_frame_without_external_file()