v0.0.6 - MMCore, OME-NGFF, and more.

v0.0.6 - Enhanced Device Support, File Types, and Documentation

We're thrilled to announce the release of v0.0.6, which includes significant enhancements and new features to improve the functionality and usability of navigate.

What's Changed?

Additional Hardware Support

We have expanded our hardware support to include ASI MCF2000, ASI MS2000, Thorlabs KCube Stepper motors, Photometrics Iris 15B, and Hamamatsu ORCA Fire. These additions significantly broaden the range of devices compatible with navigate, enhancing its versatility for various imaging setups.

New Plugin for MMCore-Based Devices

A new plugin has been developed to enable access to MMCore-based devices from Micro-Manager. This initial release supports MMCore-based stages and shutters, with future updates planned to include additional device classes such as cameras and lasers. This integration simplifies the process of incorporating a wide range of hardware into your imaging workflows.

OME-Zarr Data Source Support

We have included support for writing to the OME-Zarr data source, which enhances data management capabilities by providing a scalable, cloud-friendly format for large imaging datasets.

Documentation Overhaul

Significant updates have been made to our documentation, including:

• More examples of microscope implementations using navigate.
• Benchmarks for data writing speeds across different formats.
• Detailed guides on adding new devices.
• Instructions on using the ilastik plugin for image-based feedback.
• A comprehensive walkthrough of the software architecture and GUI.
• And more...

Improved Usability

To streamline adoption, we have created a GUI-based setup wizard and simplified the configuration.yaml file, making it easier for users with little to no programming experience to set up and use navigate.

Contributors

• @ConnorHoyUTSW
• @AdvancedImagingUTSW
• @zacsimile
• @annie-xd-wang
• @mehr0096
• @DaetwylerStephan
• @EvoleneP
• @SJShep
• @nng-thienphu

Full Changelog: v0.0.5...v0.0.6

We look forward to your feedback on these improvements!

• The Dean Lab

v0.0.5 - Timing Operations Overhaul

v0.0.5 - Timing Operations Overhaul

We're excited to announce the release of v0.0.5, which includes a significant overhaul of our data acquisition card timing operations.

What's Changed?

In previous versions, the data acquisition card executed tasks based on the cycle time, which included the exposure time plus any additional delays. These delays were inherently determined by the camera exposure time as a percent. For example, the flyback time was previously set as ~10% of the exposure time. Nonetheless, the flyback time, which typically involves a galvo or a piezo, should not depend upon the exposure time but rather the amplitude of the movement, and should be a fixed value.

New Improvements

With v0.0.5, we've revamped this approach to allow for more precise and faster imaging, with significantly reduced dwell times. This enhancement means that our timing operations are now more efficient and better suited to the needs of high-speed imaging.

We look forward to your feedback on these improvements!

Contributors

• @BingyingChen made their first contribution in #224
• @HoneybeeATc made their first contribution in #337
• @JinlongL made their first contribution in #505
• @3vwylie made their first contribution in #539
• @mehr0096 made their first contribution in #557
• @EvoleneP made their first contribution in #672
• @conorhughmcfadden made their first contribution in #699

Full Changelog: v0.0.1-alpha...v0.0.5

Pre-Model Refactor

This release aims to create a stable build prior to the major refactoring of the Model. Below are the pull requests and change-log.

What's Changed

• Yaml refactor by @AdvancedImagingUTSW in #31
• Cam view by @codeCollision4 in #35
• Add multi_position controller by @annie-xd-wang in #40
• Camera attempt by @AdvancedImagingUTSW in #43
• Refactored experiment.yml by @annie-xd-wang in #42
• First pass with laser base by @AdvancedImagingUTSW in #44
• Model in process test merge by @AdvancedImagingUTSW in #51
• Model in process by @annie-xd-wang in #50
• Swampland 2 by @AdvancedImagingUTSW in #57
• Evaluation of Widget List by @AdvancedImagingUTSW in #60
• Log changes by @zacsimile in #75
• Logging on Model, Controller, and View by @Rapuris in #76
• Logger now works on Model by @codeCollision4 in #78
• First approx camera noise model by @zacsimile in #79
• GitHub Action for running unit tests by @zacsimile in #82
• Synthetic hardware test by @zacsimile in #83
• Add codecov by @zacsimile in #84
• Add codecov by @zacsimile in #85
• Fix codecov path by @zacsimile in #86
• Remove CUDA from workflow by @zacsimile in #87
• #81 Error handling now in place by @codeCollision4 in #93
• Updates for the Camera View - Lookup Table by @AdvancedImagingUTSW in #94
• Update image saving workflow by @annie-xd-wang in #95
• Dax dev - Thread Names and Zarr wireup by @AdvancedImagingUTSW in #102
• Move from src to src/aslm by @zacsimile in #104
• Fix refactor by @zacsimile in #105
• Propagate remaining changes by @zacsimile in #106
• Startup functions tweak by @zacsimile in #108
• Basic Setup.py by @codeCollision4 in #111
• Dax dev - Zarr Implementation/Created dummy model/Updated paths for packaging by @codeCollision4 in #113
• Log and synthetic hardware fixes by @zacsimile in #114
• Dax dev - Zarr Implementation and Test are now functional by @codeCollision4 in #120
• Reorganize model by @annie-xd-wang in #123
• Z stack upgrade by @AdvancedImagingUTSW in #124
• Cleanup and comment by @AdvancedImagingUTSW in #125
• Logging and parser by @zacsimile in #127
• Enhance setup, skip some tests by @zacsimile in #130
• Validated spinboxes by @codeCollision4 in #131
• Merge sides by @AdvancedImagingUTSW in #132
• Cleanup and comment by @AdvancedImagingUTSW in #137
• Tiling Wizard by @codeCollision4 in #139
• Lazy tiff loader for prototyping by @zacsimile in #138
• Cleanup, MoveJog and TLI_DeviceInfo by @zacsimile in #141
• WASD/Mousewheel by @Rapuris in #134
• Laser settings by @Rapuris in #142
• Automatically change resolution by @annie-xd-wang in #146
• Tiling wizard now populates multi position table by @codeCollision4 in #145
• Non live display by @AdvancedImagingUTSW in #148
• Fix for #140 by @codeCollision4 in #150
• Gui refactoring by @codeCollision4 in #156
• Validatedspin editable - Class fix by @codeCollision4 in #151
• Headless Gui Tests by @codeCollision4 in #152
• Update tests by @zacsimile in #154
• Metadata implementation by @zacsimile in #155
• Update Feature Container by @annie-xd-wang in #158
• Verbose is now removed and logger is in its place by @codeCollision4 in #161
• Gui requests post chaos by @codeCollision4 in #160
• Keystroke controller by @codeCollision4 in #167
• Random fixes + trackpad scrolling for scrollbars by @zacsimile in #168
• Redesign gui by @codeCollision4 in #171
• Dockable notebook by @codeCollision4 in #173
• Metadata and image writers by @zacsimile in #172
• Better chunking by @zacsimile in #174
• Save fixes by @zacsimile in #175
• Hover class integration by @Elepicos in #177
• Tests etc by @zacsimile in #179
• support multi-position in per-stack and per-slice by @annie-xd-wang in #181
• Add cleanup support by @annie-xd-wang in #186
• Shannon Entropy: Convert to log2 and test by @zacsimile in #184

New Contributors

• @annie-xd-wang made their first contribution in #40
• @zacsimile made their first contribution in #75
• @Elepicos made their first contribution in #177

Full Changelog: https://github.com/TheDeanLab/ASLM/commits/v0.0.1-alpha