Batch Processing

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Overview

The Batch Processing mode in Microscopy Image Browser (MIB) automates image processing steps, allowing you to create a protocol that can be applied to multiple images.

This tool supports automation of workflows, from image loading to processing and saving, with options to manually define steps or automatically detect actions performed in MIB.

Demonstration

Introduction

Batch Processing offers two primary modes of operation: when actions are automatically recorded from users operations and when user defines operations manually.

Automatic Detection

When Listen for MIB actions is checked, MIB records detectable operations (e.g., image adjustments) as protocol steps.
If Auto add to protocol is also checked, these steps are automatically added to the protocol.

Attention!

Some actions (e.g., loading/saving images) are not automatically recorded and thus must be added manually.

Manual Selection

Use the Protocol steps->Section and Protocol steps->Action dropdowns to manually select and configure steps, which can then be added to the protocol.

Service Steps

The Service steps section includes special actions like:

STOP EXECUTION: Pauses the protocol for manual intervention.
Directory/File Loops: Sequentially processes multiple images from directories or files.

Start the protocol

Start the protocol with Run protocol or from a specific step using Start from selected.

In addition, green arrow buttons can be used to

to perform the selected action
to perform the selected action and progress to the next one
see below

Protocol Panel

This panel displays and manages the protocol steps.

Show settings: Displays and edits parameters in the lower Protocol steps panel.
Duplicate: Copies the selected step below it.
Insert STOP EXECUTION event: Adds a pause step.
Move up/down: Reorders steps.
Delete from protocol: Removes the selected step.

Controls

Protocol Panel controls

: executes the selected step.
: executes and moves to the next step.
Listen for MIB actions: enables automatic detection.
Auto add to protocol: auto-adds detected actions.
Show parameters on click: displays parameters on selection (otherwise use the Show settings action from the popup menu).
: manages protocol files (supports Excel export).
Undo / Redo: reverts or reapplies changes.

Protocol Steps Panel

This panel configures individual protocol steps.
This table displays settings of the selected protocol action.

In order to modify parameters:

Select parameter to change
Modify it using controls on the right-hand side
Press Update protocol to update the selected action with the updated settings

Options

Section: selects a group of actions; in general each group combines operations that can be found in the corresponding section of MIB GUI.

Loops

Loops require a LOOP START followed by LOOP STOP.

Action: chooses a specific action within the section.
Parameters Table: shows and edits action options using widgets (e.g., value, option).
Update protocol: applies changes to the selected step.
Add to protocol: appends the step to the protocol.
Insert into protocol: inserts the step at the highlighted position.

Usage Tips

Adding Loops

To process multiple images:

Select Service steps → LOOP START (e.g., for directories).
Add processing steps (e.g., image filters).
End with LOOP STOP. See the File and Directory Demo for an example.

Limitations

Not all MIB actions are automatically detectable. Manual addition is required for operations like file loading or saving.