0.6.0

Description

🎉 Here is our new TomoBEAR-0.6.0 release 🎉

🔖 Click to compare code changes with previous version v0.5.0

⬆️ 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

🐛 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

❗ Important updates

• updated "Tutorials"
• added configuration/download files as tutorials materials

0.5.0

Description

🎉 Here is our new TomoBEAR-0.5.0 release 🎉

🔖 Click to compare code changes with previous version v0.4.1

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

⬆️ 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

0.4.1

Description

🎉 Here is patch-release TomoBEAR-0.4.1 🎉

🐛 Minor fixes were done in modules AreTomo, BinStacks and Reconstruct.

🔖 Click to compare code changes with previous version v0.4.0

0.4.0

Description

🎉 Here is our new TomoBEAR-0.4.0 release 🎉

🔖 Click to compare code changes with previous version v0.3.0

🚀 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 ~10-15x 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:
  • recorded a set of short 8-12 min video-tutorials on TomoBEAR installation and 80S ribosome (EMPIAR-10064) tutorial;
  • added contribution guidelines and tips
  • extended "Usage" and reviewed "Installation and Setup" sections;
  • added "External Software" section for dependencies installation/citation description.

0.3.0

Description

🎉 Here is our new TomoBEAR-0.3.0 release 🎉

🔖 Click to compare code changes with previous version v0.2.0

🚀 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 )

📝 Important documentation updates

• updated installation instructions
• added section describing available input file formats
• added video-tutorials on TomoBEAR installation, setup and usage

0.2.0

Description

🎉 Here is our new TomoBEAR-0.2.0 release 🎉

We would be happy if you could try it out and give us your feedback !

🔖 Click to compare code changes with previous version v0.1.2

🚀 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

📝 Documentation updates

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

⚡ Other news

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

0.1.2

🎉 We are happy to announce our first public TomoBEAR release 🎉

Important news and notes

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

🐛 Bug fixes

• AreTomo module: fixed parallelization and usage