v0.4.0

Current Status: Pre-Release

Installation

OpenFIBSEM now has a set of optional dependencies to support different applications. The following autolamella methods require some of these optional dependencies. You can install them with pip.

Method	Dependencies
On-Grid	fibsem[ui]
Trench Milling	fibsem[ui]
Waffle	fibsem[ui,ml]

Workflow

The workflows have a number of improvements and fixes:

Methods

All methods now support scan rotation (both SEM and FIB).
A Trench Milling method has been added, that allows running only the trench milling workflow. Previously, this was only available as part of the more advanced methods. A baseline trench milling protocol has been added (autolamella/protocol/protocol-trench.yaml)

Protocol

Protocols have been updated to support the changes in fibsem-v0.4.0 (see release notes for details). Loading an existing protocol should be automatically converted to support the new options. If they do not, consider it a bug, and report it to me.
There is now an option to turn off the beams after the workflows complete.
The additional milling protocol options include; milling strategy, milling alignment, milling acquisition.
You can now specify the position of each pattern independently in the protocol, by editing the pattern.point. The following example shows the default positioning of the fiducial pattern (offset in x by 25um).

milling:
    fiducial:
    -   milling:
            application_file: Si
            hfw: 8.0e-05
            milling_current: 2.0e-09
            preset: 30 keV; 20 nA
        name: Fiducial
        pattern:
            depth: 1.0e-06
            height: 1.0e-05
            name: Fiducial
            passes: null
            rotation: 45
            width: 1.0e-06
            point: {"x": 25.0e-6, "y": 0.0e-6}
        strategy: {}

User Interface

Tooltips are being added to provide a short explanation for protocol and workflow options.
The workflow summary has been improved, and now shows the status, defect reason, previously completed workflow, and next workflow for each lamella. The workflow summary also includes an estimated duration for the remaining workflows.
Mark failure has been changed to Mark as Defect, and allows you to add a note for the defect reasons (e.g. contamination, cracked, etc)
Run AutoLamella now shows a summary of the workflows to be run, and allows you to enable workflow stages / supervision. This allows you to adjust the supervision without returning to the Protocol tab.
An additional Setup Polishing stage has been added allowing batch refinement of the final polishing position before running the milling.

Minimap

The minimap ui has been updated, and should be much more performant when adding many lamella.
You can now select the number of tiles, and field of view directly.
You can now cancel the overview acquisition.
Tabs have been consolidated into a single scroll area for clarity.
The display of milling patterns on positions on the overview is now officially supported. You can enable it by selecting Display Pattern, and selecting the pattern to display.
Correlation controls are now easier to access, you can toggle them with the Enable Correlation Mode button.
Screencast from 10-02-25 13:45:00.webm

Analysis Tools

AutoLamella has always recorded data and statistics about the workflows, but it was difficult for users to access the data. We believe this data is useful for users to evaluate or summarise the workflows, and are introducing some new features to make this data easier to access.

Report Generation

You can now generate pdf report with statistics about run, summary images for each lamella. The report summarises the duration of each part of the run, and provides an overview of the operations performed on each lamella.
Generating a report will also export the underlaying data as csv into the experiment directory. This data can be used for post-run analysis or overall statistics collection.
You can enable report generation by installing the additional dependencies with pip install fibsem[reporting]

Developer Notes

The protocol object is now a dataclass, instead of a dictionary. See structures.py for details.
MicroscopeSettings (settings) is being deprecated, microscope configuration is now stored on the protocol in protocol.configuration

Experimental Features

There is now code to support specifying the milling angle as the angle between the FIB and sample stage, rather than the stage tilt. This is the conventional definition of milling angle expected by the community.
This will be enabled in the next version (v0.4.1), and will need to be updated in the protocol.

What's Changed

The Run AutoLamella will now run the entire workflow.
Added confirmation popup for saving lamella at different location that current stage position
Undercut milling stages can now be defined individually in the protocol. See protocol-waffle.yaml for an example.
Validated using 180 degrees scan rotation for on-grid and waffle method.
Failed Lamella now include a note taking section.
Default protocols now use standard Si applications files instead of custom autolamella application file.

Fixes

Unchecking Use Fiducial will now properly disable milling the fiducial.
Fixed an issue where you couldn't move the lamella after creation.
Unsupervised setup lamella is now possible for on-grid method

Full Changelog: v0.3.3...v0.3.4

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v0.4.0

Installation

Workflow

Methods

Protocol

User Interface

Minimap

Analysis Tools

Report Generation

Developer Notes

Experimental Features

What's Changed

Contributors

What's Changed

Fixes

What's Changed

What's Changed

Contributors

What's Changed

Contributors

Releases: DeMarcoLab/autolamella

v0.4.0

v0.4.0

Installation

Workflow

Methods

Protocol

User Interface

Minimap

Analysis Tools

Report Generation

Developer Notes

Experimental Features

v0.3.5

What's Changed

Contributors

v0.3.4

What's Changed

Fixes

v0.3.3

What's Changed

v0.3.2

v0.3.1

v0.2.5

What's Changed

Contributors

v0.2.4

What's Changed

Contributors

v0.2.3

v0.2.2