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Version 0.1.3.1
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@ffvoigt ffvoigt released this 13 Mar 09:39
· 734 commits to master since this release
0.1.3.1
5af2b6e

Important Changes

  • ⚠️ Depending on your microscope configuration, this release breaks backward compatibility with previous configuration files. If necessary, update your configuration file using demo_config.py as an example.
  • ⚠️ There are new startup parameters in the config file - make sure to update your config files accordingly. For example, average_frame_rate has been added.
  • ⚠️ This release removes unnecessary configuration files from the public repository - make sure to back up your mesoSPIM & ETL configuration files beforehand. In addition, old example acquisition tables (in mesoSPIM-control\mesoSPIM\acquisitions\) are removed as well.

New Features

  • 💎 New: Support for more cameras: Photometrics cameras are now supported if PyVCAM and the PVCAM-SDK are installed. Only the Iris 15 has been tested so far. In addition, the Hamamatsu Orca Fusion is now supported.
  • 💎 New: Multicolor tiling wizard: The Tiling wizard can now support up to 3 color channels with different ETL parameters and focus tracking settings.
  • 💎 New: Full demo mode - addresses #16: mesoSPIM-control can now be run without any microscope hardware by using the demo_config.py configuration file.
  • 💎 New: Snap function -- Single pictures can now be taken by clicking the snap button. The filename is autogenerated from the current time. Files are saved as .tif which requires tifffile as an additional library.
  • 💎 New: Acquisition time prediction -- mesoSPIM-control now measures the average framerate every 100 frames to predict the acquisition time. To have a correct initial estimate
    in the Acquisition Manager, please update the average_frame_rate with the measured values
    from your microscope (are now logged in the metadata files after an acquisition).
  • 💎 New: Focus tracking -- Different start and end focus positions can now be specified in the Acquisition Manager. When moving the sample to acquire the stack, the microscope changes focus according to a linear interpolation between these values. At z_start, the microscope moves the detection path
    to f_start and at z_end, the detection path focus is at z_end. This allows imaging a liquid-filled sample cuvette without an immersion cuvette. The Mark current focus button changes both values at once.
  • 💎 New: Improved acquisition previews -- An additional checkbox allows to switch off Z axis movements when previewing acquisitions. This way, the field-of-view does not move outside of the sample which is especially helpful when updating ETL value for individual tiles/stacks in large acquisition tables. ⚠️ When previewing an acquistion requires a rotation, z movements still occur for safety reasons.
  • 💎 New: Image Processing Wizard: mesoSPIM-control now has an Image Processing Wizard (accessible via a button in the Acquisition Manager). Currently, this allows maximum projections to be generated automatically after acquisitions.

Improvements

  • ✨ Improvement: Acquisition Manager: Naming of buttons has been improved, in addition, tooltips have been added to improve usability.
  • ✨ Improvement: Removed unnecessary microscope and ETL configuration files cluttering the repository. Changed .gitignore correspondingly - future changes to configuration files. This addresses issue #16.
  • ✨ Improvement: The software now provides more verbose warnings when acquisitions cannot be started due to missing folders, duplicated filenames and already existing files.
  • ✨ Improvement: Better warnings if no row is selected while clicking Mark buttons.
  • ✨ New: Added a CHANGELOG.md file

Bugfixes

  • 🐛 Bugfix: Manually entering a value in a field in the Acquisition Manager table would change values in other rows as well if the row had been copied before.
  • 🐛 Bugfix: Mark buttons and dropdown menus in the Acquisition Manager table slowed down the GUI when a lot of rows (>25) were present. As a fix, only the selected row shows the menu.
  • 🐛 Bugfix #26: Fixed: First row is selected by mark buttons by default if only a single row exists in the Acquisition Manager Table
  • 🐛 Bugfix #27: Fixed: Entering text into boxes is a bit buggy
  • 🐛 Bugfix #30: Fixed: Zooming drop down menu often fails to update after a zoom
  • 🐛 Bugfix #31: Fixed: demo_config.py now contains subsampling settings
  • 🐛 Bugfix #34: Fixed: Last frame in a stack is blank due to an off-by-one error
  • 🐛 Bugfix #35: Fixed: Software crashes when one folder (to save data in) in the acquisition list does not exist
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