This documentation is for the older Mesmerize legacy desktop application. Please see the home page or GitHub repo for information on the latest packages.

Add a Sample to the Project

When you are happy with the ROIs in the viewer for the current CNMF(E) derived or manually created ROIs, you can add this as a Sample to your project.

Each sample in your project contains the following:

  • The imaging data from which ROIs were extracted (the video)

  • All the ROIs with their spatial location, temporal dynamics, and any tags that you have entered in the ROI Manager.

  • Stimulus mappings, if your project is configured for this.

  • Meta data (that were associated with the imaging video), the date, video framerate.

  • Any further information that you have chosen to add based on your Project Configuration


If your ROIs were obtained through CNMF/CNMFE the following attributes from the final cnm object are stored: cnm.A, cnm.b, cnm.C, cnm.f, cnm.YrA

How to

To add the current viewer work environment (see above) as a sample to your project, go to File -> Add To Project. You will be presented with a window similar to this:


The entries that you are prompted with directly correspond to the custom columns in your Project Configuration.

Every Sample in a project has a unique SampleID which is the combination of AnimalID + TrialID.


You can never change the AnimalID or TrialID (i.e. SampleID) since these are partially used as unique identifiers. A workaround is described in the FAQ for Project Organization.


AnimalID and TrialID are separated by the -_- character combination when stored as a SampleID. Therefore do not use that character combination within your AnimalID or TrialID.

Video Tutorial