tomotools - v0.4.5

What's Changed

• fixed bug with weirdly named Tomo5 mdocs, see issue #50 by @bwmr in https://github.com/tomotools/tomotools/pull/51

Full Changelog: https://github.com/tomotools/tomotools/compare/v0.4.4...v0.4.5

- Python
Published by bwmr 11 months ago

tomotools - v0.4.4

• Bugfix: tomotools preprocess now raises an error, if frame paths are specified in mdoc but the corresponding files are not found.

Full Changelog: https://github.com/tomotools/tomotools/compare/v0.4.3...v0.4.4

- Python
Published by bwmr about 1 year ago

tomotools - v0.4.3

What's Changed

• AreTomo2/MotionCor3 support by @bwmr in https://github.com/tomotools/tomotools/pull/43
• Important Bugfix: during AreTomo alignment, the alignment thickness was not calculated correctly -> now fixed!

Full Changelog: https://github.com/tomotools/tomotools/compare/v0.4.2...v0.4.3

- Python
Published by bwmr over 1 year ago

tomotools - v0.4.2

What's Changed

• Fixed export to Warp with and without frames by @bwmr in https://github.com/tomotools/tomotools/pull/45
• tomotools preprocess can now run with only an mdoc file, if frames are listed in it. Required for Tomo5 support, see issue #42

Full Changelog: https://github.com/tomotools/tomotools/compare/v0.4.1...v0.4.2

- Python
Published by bwmr over 1 year ago

tomotools - v0.4.1

• Fixes for WarpTools 2.X compatibility in imod2warp /aretomo2warp Full Changelog: https://github.com/tomotools/tomotools/compare/v0.4...v0.4.1

- Python
Published by bwmr over 1 year ago

tomotools - v0.4

What's Changed

• Make Frames available to Warp in STA workflow by @bwmr in https://github.com/tomotools/tomotools/pull/41

Full Changelog: https://github.com/tomotools/tomotools/compare/v0.3.4...v0.4

- Python
Published by bwmr over 1 year ago

tomotools - v0.3.4

What's Changed

• Fix for issue #37 by @bwmr in https://github.com/tomotools/tomotools/pull/39
• Rename batch-prepare-tiltseries to preprocess by @bwmr in https://github.com/tomotools/tomotools/pull/40

Full Changelog: https://github.com/tomotools/tomotools/compare/v0.3.3...v0.3.4

- Python
Published by bwmr almost 2 years ago

tomotools - v0.3.3

What's Changed

• Binning Options for x2tomotwin by @alicethurston in https://github.com/tomotools/tomotools/pull/33
• Bugfix: tilt order in imod2warp by @MoritzWM in https://github.com/tomotools/tomotools/pull/34
• initial implementation of tomotools reconstruct-3dctf by @bwmr in https://github.com/tomotools/tomotools/pull/30

New Contributors

• @alicethurston made their first contribution in https://github.com/tomotools/tomotools/pull/33

Full Changelog: https://github.com/tomotools/tomotools/compare/v0.3.2...v0.3.3

- Python
Published by bwmr almost 2 years ago

tomotools - v0.3.2

New Features

• export (lists of) tomograms to TomoTwin using aretomo2tomotwin and imod2tomotwin

Minor Changes

• git-lfs is no longer required for installation
• reconstruct:
  • --previousnow respects the alignment flag--imod/--aretomo[default]`
  • new flag --do-positioning/--skip-positioning[default]
• README.md now clearly lists which (third-party) software packages are required to be installed and on PATH

Fixes

• cryocare-predict now only outputs tiltseries once, instead of twice
• reconstruct:
  • naming issue fixed for AreTomo alignment file when input tiltseries had suffix .st
  • binned stack is now deleted after reconstruction
• batch-preapre-tiltseries: --exposuredose is now actually written to mdoc

PR merged in this release

• Install dependencies by @McHaillet in https://github.com/tomotools/tomotools/pull/23
• Fix install nogitlfs by @bwmr in https://github.com/tomotools/tomotools/pull/28
• Prepare files for TomoTwin by @bwmr in https://github.com/tomotools/tomotools/pull/31

New Contributors

• @McHaillet made their first contribution in https://github.com/tomotools/tomotools/pull/23

Full Changelog: https://github.com/tomotools/tomotools/compare/v0.3.1...v0.3.2

- Python
Published by bwmr over 2 years ago

tomotools - v0.3.1

Features

• in tomotools reconstruct, more options can be given:
  • total thickness (--thickness/-d)
  • conversion to bytes (--bytes/--nobytes)
  • AlignZ for AreTomo (--ali-d)
• optimized imod2warp

Functions

• functions to edit comfiles, including ability to create ctfcorrection.com and tilt.com for AreTomo-aligned stacks
• ability to perform reconstruction with 3D CTF using imod ctf3d

Changes

• skip-positioning is now default during reconstruction
• XY dimensions of tomogram are now correctly calculated based on binning and rotation axis
• newstack is used for binning aligned stacks

This branch was a long time in the making, but in order to move to more focused, feature-specific branches, these are the main changes (additional changes were moved to relion4 and stopgap branches and subtomotools directory).

What's Changed

• Updates to main by @bwmr in https://github.com/tomotools/tomotools/pull/21 Full Changelog: https://github.com/tomotools/tomotools/compare/v0.3...v0.3.1

- Python
Published by bwmr over 2 years ago

tomotools - v0.3

Release 0.3 with the following updates:

Added Functions

• fit-ctf command to run ctfplotter
• imod2warp / aretomo2warp workflows to export tiltseries for STA, including ability to fix SerialEM > 4 mdoc files.

Convenience

• Tomogram reconstruction can now be done with trimming, but without conversion to byte (in Tomogram.from_tiltseries).
• Improved legibility of terminal output.
• - AreTomo now takes lamella pretilt into account for alignments (but not reconstructions).
• EVN/ODD stacks are now called even / odd so imod can automatically find them.

Fixes

• AreTomo Multi-GPU processing works again.
• Support for DarkImages files from AreTomo > 1.3.
• Bugfix parsing .aln files containing local alignments.
• Removed unused files remaining from before refactoring code in v0.2.
• RotationAndFlip conversion error was brought back during linting, now finally banished.

Particle projection and star-file handling were moved to new repository subtomotools :)

- Python
Published by bwmr over 2 years ago

tomotools - v0.2.4

Same as v0.2.3, but freshly linted and with pyproject.toml instead of setup.py

- Python
Published by bwmr over 2 years ago

tomotools - v0.2.3

Changes in batch-prepare-tiltseries command:

• Make patch frame alignment optional and non-default. Probably it induces overfitting as tilt frames usually have very little dose / SNR. Inspired by the Warp tutorial.
• Pre-existing frames-corrected directory is now overwritten. This was a common source of errors if the frame alignment crased or was stopped between tiltseries.
• Rename --gpus to --gpu for consistency.

Other changes:

• added semnavigator function to quickly render positions of items and maps in SerialEM .nav files.

- Python
Published by bwmr about 3 years ago

tomotools - v0.2.2

New

• perform EVN/ODD reconstruction based on previous imod alignment
• AreTomo 1.3.0 compatibility

Fixed

• RotationAndFlip is now correctly translated to -RotGain / -FlipGain. this means you may need to re-do gain correction if the RotationAndFlip value was uneven
• crash if no gain reference was provided or gain reference as mrc
• deconv now actually works

- Python
Published by bwmr over 3 years ago

tomotools - v0.2

Major rewrite to be object-based. Supports easy processing of EVN/ODD stacks, cryoCARE extraction, ... Requires Python 3.8 for cryoCARE compatibility.

- Python
Published by bwmr over 3 years ago

tomotools - v0.1.1

Initial release with tested functions for pre-processing and batch reconstruction.

- Python
Published by bwmr over 3 years ago