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Recent Releases of tomobear

tomobear - 0.6.0

Description

:tada: Here is our new TomoBEAR-0.6.0 release :tada:
:bookmark: Click to compare code changes with previous version v0.5.0

:arrow_up: Improvements

  • enabled ST files import
  • AreTomo: write truncated (raw)tlt file(s) omitting excluded views
  • Reconstruct: enable usage of truncated (raw)tlt files
  • EMDTemplateGeneration: (forced) pixel size to be used

:bug: Important fixes

  • GCTFCtfphaseflipCTFCorrection: fix ctfphaseflip input pixel size unit
  • Reconstruct:
    • produce tomograms only at the requested binning
    • adjust exact filter size according to binning
  • IsoNet: fix defocus units in STAR file
  • EMDTemplateGeneration: fix mask generation based on deposited EMDB mask
  • DynamoAlignmentProject: fixed Dynamo Current Project integration

:exclamation: Important updates

- MATLAB
Published by ArtsemiY about 2 years ago

tomobear - 0.5.0

Description

:tada: Here is our new TomoBEAR-0.5.0 release :tada:
:bookmark: Click to compare code changes with previous version v0.4.1

A brief description of the most important changes you can find below.

:arrow_up: Improvements

  • Reconstruct: enabled SIRT and FakeSIRT reconstructions
  • crYOLO | IsoNet: enabled specifying conda environment by custom environment path (e.g. group-shared conda env)
  • general: added parameter to control number of digits for TS slices file naming

- MATLAB
Published by ArtsemiY over 2 years ago

tomobear - 0.4.1

Description

:tada: Here is patch-release TomoBEAR-0.4.1 :tada:

:bug: Minor fixes were done in modules AreTomo, BinStacks and Reconstruct.
:bookmark: Click to compare code changes with previous version v0.4.0

- MATLAB
Published by ArtsemiY over 2 years ago

tomobear - 0.4.0

Description

:tada: Here is our new TomoBEAR-0.4.0 release :tada:
:bookmark: Click to compare code changes with previous version v0.3.0

:rocket: 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

:arrow_up: 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)

:bug: Important fixes

  • DynamoTemplateMatching: :exclamation: fixed bug preventing GPU-enabled ~10-15x speedup :exclamation:

:exclamation: 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:

- MATLAB
Published by ArtsemiY almost 3 years ago

tomobear - 0.3.0

Description

:tada: Here is our new TomoBEAR-0.3.0 release :tada:
:bookmark: Click to compare code changes with previous version v0.2.0

:rocket: 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

:arrow_up: 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

:bug: Major fixes

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

:pencil: Important documentation updates

- MATLAB
Published by ArtsemiY about 3 years ago

tomobear - 0.2.0

Description

:tada: Here is our new TomoBEAR-0.2.0 release :tada:
We would be happy if you could try it out and give us your feedback !
:bookmark: Click to compare code changes with previous version v0.1.2

:rocket: 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.

:arrow_up: Improvements

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

:bug: 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

:pencil: Documentation updates

  • minor fix in in the tutorial JSON file shipped with cloned repository
  • upd instructions on AreTomo-based projects configuration in Usage

:zap: Other news

  • (upd) The next minor version v0.3.0 release is planned for late-March/early April 2023. Stay tuned!

- MATLAB
Published by ArtsemiY over 3 years ago

tomobear - 0.1.2

:tada: We are happy to announce our first public TomoBEAR release :tada:

Important news and notes

  • :package: standalone executable is released! available for usage on GPU workstations (:books: documentation on setup and usage)
  • :construction: unfortunately, standalone is not working yet on interactive cluster sessions! we are working to resolve that.

:bug: Bug fixes

  • AreTomo module: fixed parallelization and usage

- MATLAB
Published by ArtsemiY over 3 years ago