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MagellanMapper v1.3.5
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@yoda-vid yoda-vid released this 06 Aug 11:45
· 1929 commits to master since this release
v1.3.5
d362f0c

This release streamlines refreshing and overlaying images through the GUI. Workarounds are also provided for several installation/dependency issues.

Changes

GUI

  • Multiple intensity images can be selected through the GUI to overlay
  • Refreshes images in each viewer after a new image has been loaded
  • Selecting an ROI dropdown menu entry updates the current viewer
  • Fixed retaining prior images and resolutions from previously loaded image during the session
  • Fixed setting the initially displayed channel from the command-line
  • Fixed to show the labels reference file if loaded from command-line
  • Fixed loading ROI Editor layouts with 3D screenshots if the 3D viewer had not been opened yet
  • Fixed 3D viewer orientation when opening the tab for the first time during a session
  • Fixed blob detections to appear in both the ROI Editor and 3D viewer

CLI

  • Simplify loading only images by registration suffix to allow specifying a directory as such: --img <dir> --reg_suffixes [atlas-img] [annotation-img]

I/O

  • Resolutions are easier to read with fewer decimal places shown
  • Filenames are saved in the database experiments table without extension to allow more naming flexibility
  • Fixed applying objective magnification and zoom metadata to multi-plane image imports

Server pipelines

  • Removed default microscope objective metadata now that metadata is extracted from input files when possible

Python stats and plots

  • Fixed loading discrete, symmetric colormaps with an even number of colors

Dependency Updates

Python Dependency Changes

  • PyQt is now specified explicitly for Conda environment installs to avoid installing an older release (ie was installing v5.9 instead of v5.12)
  • Matplotlib v3.2 is installed because of performance slowdown especially during mouseover of images when using the latest current release (v3.3)
  • Fixed setup.py to include PyYAML (dependency introduced in MagellanMapper v1.2.1)

Server dependency Changes

  • Dockerfiles are included, with one version based on Miniconda3 and another on Ubuntu 18.04
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