Batch Manager

Batch process computationally intensive tasks.

This is currently used for Caiman Motion Correction, CNMF, 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.

Colors Description
Green Finished without exceptions
Red Did not finish, click on the item to see the exceptions in the bottom right information area
Yellow Currently being processed
Orange Item aborted by user
Blue Output data for this item are being moved from the work dir to the batch dir.
Button Description
Start 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 Abort the current batch item
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
Compress Not implemented

Use work dir: Check this box to use the work dir that has been set in the System Configuration

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