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

Batch Manager

Batch process computationally intensive tasks.

Video Tutorial

This tutorial shows how to create a New Project, open images in the Viewer, use the Stimulus Mapping module and perform Caiman motion correction

This is currently used for Caiman Motion Correction, CNMF, CNMF 3D and CNMFE.

The Batch Manager can be accessed in the viewer through Modules -> Batch Manager. If you don’t have a batch open you will be prompted with a dialog to open a batch or to select a location for a new batch.


The full path to the batch directory must not contain spaces or special characters, only a-z, A-Z, 0-9 and underscores.

The Batch Manager processes the batch items in external processes, allowing you to add batch items when that batch is being processed.



Window title: Name of batch directory

Top: Parent directory of batch directory

Top left: list of batch items and some controls.




Finished without exceptions


Did not finish, click on the item to see the exceptions in the bottom right information area


Currently being processed


Item aborted by user


Output data for this item are being moved from the work dir to the batch dir.




Process the batch from the first item.

Start at selection

Process the batch starting from the item that is currently selected in the list.

Delete selection

Delete the item that is currently being selected along with the associated data in the batch dir.

Export shell scripts

Export bash scripts so that the batch items can be run on a computing cluster

Abort current item

Abort the current batch item and move on to the next item

Abort batch

Abort the current item and stop processing the batch

New batch

Create a new batch

Open batch

Open a batch

View Input

Open the input work environment, in the viewer, for the currently selected item

Use work dir: Check this box to use the work dir that has been set in the System Configuration. This feature is only available on Linux & Mac OSX.

Top right: Standard out from the external processes that are processing the batch items.

Bottom left: Parameters for the selected batch item. The first line is the UUID of the batch item.

Bottom right: Output information area for the currently selected item.


You can schedule a batch to run at a later time using the following bash script. Doesn’t work for a snap installation yet.



Usage: mesmerize-scheduler -b <batch> -i <start item> -t <start time>

    -b      full batch path in quotes, no spaces
    -i      uuid of the batch item to start from, no quotes
    -t      time at which to start the batch, no quotes

    examples of how to specify time:
            23:00  7:30Feb30
            use 24hr time and no spaces

Full usage example:
    mesmerize-scheduler -b "/share/data/temp/kushal/pc2_batch" -i a80d1923-e490-4eb3-ba4f-7e651d4cf938 -t 2:00