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CHANGELOG.md

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Changelog

All notable changes will be documented in this file.

v0.4.0 - 2023-08-07

🚀 New Features

  • crYOLO - module wrapping crYOLO - DL tool, based on You Only Look Once (YOLO) object detection system for predicting particle coordinates (basically picking them) in cryo-electron tomograms

⬆️ Improvements

  • IsoNet: added possibility to post-process IsoNet-corrected tomograms using NAD filtering
  • DynamoTemplateMatching: enabled usage of the tomograms from the custom user-provided path
  • AreTomo:
    • enabled direct usage of AreTomo alignment parameters from previously executed AreTomo step
    • enabled parameters: tilt axis offset (pre-tilt) and temporary reconstruction thickness (VolZ)

🐛 Important fixes

  • DynamoTemplateMatching: fixed bug preventing GPU-enabled speedup

❗ Important updates

  • changed license of the core code base from AGPLv3 to GPLv3 - changed license to a bit more permissive version in order to allow software maintainers and other TomoBEAR contributors more flexibility in terms of TomoBEAR modifications, needed to provide a TomoBEAR operation over local networks (like institutional intranets and/or shared filesystems);
  • updated documentation:

v0.3.0 - 2023-05-22

🚀 New Features

  • local_live data processing mode - new mode allows to make on-the-fly pre-processing and reconstructions during data collection to check the sample quality. Currently only single-shot collected data is supported for this feature.
  • EER (Electron Event Representation) support: input files format perception along with .gain gain file format support are now enabled in MotionCor2 module
  • GenerateParticles - new module which allows to generate particles using either Dynamo (by cropping) or SUSAN (by subtomogram reconstructions)
  • IsoNet - module wrapping IsoNet - CNN for denoising and missing wedge reconstruction

⬆️ Improvements

  • BinStacks: added possibility to bin non-aligned stacks
  • AreTomo:
    • enabled binned stack input
    • enabled local patch-based alignment
  • BatchRunTomo: enabled IMOD-based patch-tracking
  • Reconstruct: enabled nonlinear anisotropic diffusion (NAD) filter for tomograms post-filtering
  • GCTFCtfphaseflipCTFCorrection: added possibility to use CTFFIND4

🐛 Major fixes

  • input files perception - fixed duplicated file extension ( issue #16 )

v0.2.0 - 2023-02-23

🚀 New Features

  • GridEdgeEraser: a new module which allows to identify position of the grid edge and mask it out.
    • Currently only gold grids data is supported for this feature.

⬆️ Improvements

  • AreTomo:
    • enabled IMOD-compatible files output
    • enabled tilt axis offset parameter

🐛 Fixes

  • EMDTemplateGeneration: fixed EMDB URL
  • BatchRunTomo: fixed bug which prevented running TomoBEAR project for a single tilt serie
  • GCTFCtfphaseflipCTFCorrection:
    • fixed AreTomo-aligned data usage
    • fixed aligned stack usage
    • fixed Ctfphaseflip usage
  • Reconstruct: fixed reconstruction based on AreTomo-aligned data

v0.1.2 - 2023-01-20

🐛 Fixes

  • AreTomo module: fixed parallelization and usage