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



  1. Can I delete an ROI?
  2. I don’t want to delete ROIs but I want to mark them for exclusion in further analysis, how can I do this?
    • You can do this by creating an ROI type category. See <link here> Add New ROI Type Later which uses this as an example. You can also create this ROI Type category when you create a New Project, not necessarily when you already have a project as the example uses.

  3. Can I tag more than one piece of information to each ROI?
    • Yes, add as many ROI Type categories as you want in the Project Configuration.

  4. I already have a Mesmerize project with many Samples in it. Can I add a new ROI Type category?
  5. Can some samples in my project have ROIs that originate from CNMF(E) and others that are manually drawn?
    • Yes, but be aware that you may need to separate the CNMF(E) and manual data in downstream analysis if using flowchart nodes that work with data from specific sources.


  1. I have ROIs that clearly encompass multiple cells instead of just one
    • Increase min_coor

    • Might help to reduce gSig as well

  2. I have too many bad ROIs around random regions that are clearly noise
    • Increase min_pnr

  3. Min_PNR image is completely blue and void of any signals
    • Increase gSig

  4. Vmin slider is stuck in Inspect Correlation & PNR GUI.
    • Close and reopen it. This is a matplotlib issue, not something I can fix.

Caiman Motion Correction

  1. I have video tearing
    • Try increasing upsample grid

    • It’s possible that the movement is too severe to be motion corrected. When the movement is so severe that the information do not exist, it is impossible to motion correct it.

  2. My animal is growing
    • This is growth, not motion. Unfortunately cannot be corrected for. If you have an idea for a technique I can try it out.

  3. The output actually has more motion, it has created false motion.
    • Try these things:
      • Reduce Strides & Overlaps by ~25%

      • Reduce max shifts X & Y by ~25%

      • Reduce max deviation from rigid by ~25%

Project Organization

  1. Can I modify a sample?
    • Yes. Double click the Sample ID in the Project Browser to open it in a viewer. You can then make any modifications you want and then go to File -> Add to Project and select the “Save Changes (overwrite)” option at the bottom. If you have not changed the image sequence itself you can uncheck “Overwrite image data”.

  2. Can I change the SampleID?
    • No this is fundamentally impossible.

    • A work-around is to open that Sample in the viewer (double click it in the project browser), make any modifications if necessary, then go to File -> Add to Project, enter the the information for this sample and a new Animal ID (and Trial ID if wanted), and then select the option “Add to Project Dataframe” at the bottom and click Proceed. This will now add a new Sample to the project with this Sample ID. You can then delete the previous Sample.

  3. Can I add a new Custom Column, ROI Column, or Stimulus Column to my project when I already have samples in my project?
    • Yes, just modify your Project Configuration. In the Welcome Window go to Configure -> Project Configuration. Add anything that you want, and then click “Save and Apply”. It’s best to immediately restart Mesmerize whenever you change your project configuration.

    • If you are adding a new Custom Column you can enter a “Dataframe replace value”. This will allow you to set a value for all existing Samples in your project for this new column.

    • If you do not set a Dataframe replace value it will label all existing as “untagged”