Changelog
Contents
Changelog¶
Legend: New feature, Improvement, Bug fix
v0.6.2 (2/01/2024)¶
Expose additional parameters for frame alignment when using MotionCor3.
Remove unnecessary tabs from tomography refinement blocks.
Display slurm job launch information in the logs window.
Allow users to specify resources for the launch task on the Sessions side.
Fix bugs in parameter definitions when running movie frame alignment.
Fix bugs in the management of slurm’s GRES options when submitting jobs to the scheduler.
Fix bug with movie drifts being deleted from the database when tilt-series were re-processed.
v0.6.1 (1/30/2024)¶
Produce metadata for 3D visualization using ArtiaX for all refinement blocks. See the user guide for details.
Enable dose weighting and magnification correction options during frame alignment and averaging.
Allow specification of SLURM account for all job types to improve portability.
Expose full set of options when using MotionCor3 for frame alignment.
Allow specification of GPU resources using Gres option to allow selection of specific types of graphics cards, e.g., gpu:A100:1.
Add support for multiple date formats when reading metadata from .mdoc files.
Add support for .gain reference files and automatically resize corresponding .eer movies in data import blocks.
Fix issue when handling *.tif files that have a *.tiff extension.
Fix issue with multiprocessing library when using NFS mounts as local scratch.
Fix bug in single-particle sessions when using unbinned images for 2D classification.
Fix bug when picking particles using neural network-based approach on non-square tomograms.
Fix bug that prevented GPU jobs from running because the jobs were sent to the CPU queue.
v0.6.0 (1/21/2024)¶
Allow use of MotionCor3 for movie frame alignment (GPU required).
Allow use of AreTomo2 for tilt-series alignment and reconstruction (GPU required).
Allow use of Topaz for 2D particle picking and 3D denoising (GPU recommended).
Produce .bild files after each refinement iteration for 3D visualization in Chimera/ChimeraX.
Automatic determination of CTF handedness during pre-processing of tilt-series.
Allow mix-and-match of IMOD and AreTomo2 for tilt-series alignment and tomogram reconstruction.
Automatically submit jobs to a GPU partition when running tasks that require GPU acceleration.
Display version number and amount of allocated memory at the beginning of every job.
Change default memory allocation for launch task to 4GB and add Resources tab to all data import blocks.
Simplify Resources tab by hiding unnecessary parameters depending on the block type.
Implement GPU resource management policies for slurm and standalone modes.
Show per-particle score distribution for all tomography refinement blocks and improve plot layout.
Allow use of slurm’s GRES (generic resource scheduling) when submitting jobs to a cluster.
Fix OOM error when running constrained refinement using a single thread.
Fix error in particle filtering blocks when no particles are left in a given micrograph/tilt-series.
Fix issue in tomography sessions when .mdoc files are not used to import metadata.
Fix bug when exporting sub-tomograms for use in external programs.
Update systemd script to improve robustness during program restart.
Fix issues with cancellation of jobs in standalone mode.
Fix discrepancy with gain reference rotation/flips between data import and pre-processing blocks.
v0.5.3 (11/25/2023)¶
Implement interactive measuring tool for micrographs and tomograms.
Allow multiple sessions when user login mode is enabled.
Sort classes in increasing order in Class View panel.
Fix issues when limiting total number of tasks in slurm scheduler.
v0.5.2 (11/18/2023)¶
Add support for PACEtomo tilt-series in streaming Sessions.
Parallelize reconstruction step during 3D classification for faster speeds.
Add new options to flip maps in post-processing block.
Simplify installation instructions and setup process.
Fix issue with location of executables for neural network-based particle picking.
Fix issue with re-calculation of binned tomograms when reconstruction parameters change.
Fix issue with re-calculation of particle coordinates when no particles were found.
Correctly display particle size in tomography pre-processing block statistics.
v0.5.1 (11/04/2023)¶
Import frame tilt-series data using mdoc files produced by PACEtomo.
Allow typing iteration number in navigation bar for refinement blocks.
Show refinement/bundle IDs in
Per-particle ScoreandExposure Weightstabs for refinement blocks.Fix issue with display of tomograms with arbitrary thickness.
Fix broken CLI commands and update CLI tutorials.
v0.5.0 (10/26/2023)¶
This was the first release of nextPYP.