ver5.1: improved amyloid processing and minor updates to tomography pipeline

This release implements new functionality for amyloid filaments:

• a new auto-picker that specifically detects the 4.75A signal in the Fourier transform of micrographs
• amyprep and amyproc Schemes for the automated pre-processing of amyloid data sets
• a retrained version of the Blush regularisation denoising network that is specific for amyloid filaments

This release also implements minor updates to the tomography pipeline, including:

• a wrapper to AreTomo2's tomogram reconstruction algorithm
• an option to extract real 3D subtomograms (this goes well with the AreTomo2 reconstructions), and to use these for 3D classifications/refinements. (Some people like this for getting initial 3D subtomogram averages.)

RELION 5.0.1

This is the first maintenance release of RELION 5.0. We recommend all RELION users to upgrade to this version, because this fixes bugs and improves the compatibility.

Compiler compatibility

In RELION 5.0.1, we added support for CUDA >= 12.9. This means CUDA 11.x, 12.x and 13.x are currently supported. Please note that CUDA 13.0 no longer supports Pascal GPUs, such as GTX 1080 Ti and P100. Users of these GPUs must use CUDA 11 or 12. We no longer test CUDA 10 and earlier.

Compilation of RELION 5.0.1 requires a C++ compiler that fully supports the C++17 standard, while RELION 5.0.0 required only C++14.

As of RELION 5.0.1, you need CMake earlier than 3.27. We will fix this issue in future.

Blackwell GPUs

To use deep-learning based tools like Topaz, Blush and DynaMight, please use environment_blackwell.yml instead of environment.yml when setting up the relion-5.0 conda environment. If you already have one, please remove the existing environment by conda remove -n relion-5.0 --all and start from scratch.

What's Changed

• Fixed body placement in flex analyzer as reported by @mazoryuv
• Supported CUDA 12.9 and 13.0, patch contributed by NVIDIA engineers (Alexey Romanenko et al.)
• Improvements for AMD GPUs (HIP code path) by @suyashtn
• Improvements on oneAPI kernels by @do-jason
• SYCL optimization for cache friendly data structure by @do-jason
• Updated eer_trajectory_handler.py (fix NumPy deprecation of np.int and np.float in RELION 5 conda) by @rbs-sci
• Created environment_blackwell.yml for RTX 5000 PyTorch support by @rbs-sci
• Improved numerical precision of subtomogram extraction point projection by @daniel-ji
• Fixed 3d radial averaging by @daniel-ji
• Fixed reconstruct particle contrast inversion by @daniel-ji
• and more bug fixes (see Full Changelog at 5.0.0...5.0.1)

New Contributors

• @suyashtn made their first contribution in #1219
• @rbs-sci made their first contribution in #1271
• @daniel-ji made their first contribution in #1285

This release note was partly written by the "generate release notes" feature of GitHub.
If we missed important changes and contributors, please let us know.

relion-5.0.0 stable release

This is the first stable version of RELION 5.0. With the release of this version, earlier RELION versions (4.0.x) are no longer supported. We recommend all RELION users to upgrade to this version.

For the list of new features, please look at the What's new? page in our documentation.

We are grateful to everyone who has contributed to making relion better, including during beta-testing. A special thanks goes to @eugenejyuan, @harryswift01, @Arpan3323 and @huwjenkins

4.0.2

This is the second maintenance release of the RELION 4.0 series. We recommend all RELION users to upgrade to this version (or to 5.0 beta), because this fixes bugs, improves compatibility and introduces convenient features.

New features and bug fixes include:

• Repaired a bug in float16 conversion when the mantissa overflows upon rounding (ee46696)
• Fixed a build issue when BUILD_SHARED_LIBS=ON (Github issue #958 reported and investigated by @markus-meier74 and @do-jason) (884ff0d)
• Ensured the output prefix has the trailing "/" in MotionCorr (GitHub issue #1174 reproted by @davidheisenberg) (1441120)
• Repaired InitialModel GUI to apply C10,C11...C19 symmetry when requested as reported by @huwjenkins (c3974ae)
• Handled cases where the diameter is too big in initial blob generation (5a15339)
• Improved a confusing message about initial noise estimation as pointed out by Tsai-Hsuan Weng on CCPEM (f702524)
• Use half maps for initialization in autorefine (Github issue #1055 reported by @huwjenkins) (c61651c)
• Repaired a CRITICAL bug where OpenMP pragma omp critical was ignored (GitHub issue #1038) (dcc8fe7)
• Repaired a bug in local symmetry of auto-refine (7809a73)
• Repaired a bug in the acceleration code reported by Greta Assmann (6a708b0)
• Added --external_recosntruct as a flag for continued refinements (ed4c13c)
• Ensured twist and rise of half2 are updated upon convergence in autorefine (GitHub issue #1026 reported by @awenborn) (66e4fa0)
• Overwrite existing logfile.pdf in PostProcess (GitHub issue #1068 reported by @pherepanov) (1dc50f5)
• Fixed contrast inversion when there is no gain reference in Polish (1765b3d)
• Repaired relion_reconstruct --ewald --newbox (e16f796)
• Made frame numbers consistent (1-indexed) in relion_convert_to_tiff (0b03a6f)
• Improved parallelization in relion_convert_to_tiff --only_do_unfinished (GitHub issue #985 reported by @eMKiso) (dd10f8a, 51db1a7)
• Repaired a bug in renaming alias (e1b2456)

4.0.1

This is the first maintenance release of RELION 4.0. We recommend all RELION users to upgrade to this version, because this fixes bugs, improves compatibility and introduces convenient features.

New features and bug fixes include:

• Supported MRC movies compressed by bzip2, xz or ZStandard in RELION's motion correction and Bayesian Polish for SPA. You need pbzip2, xz or zstd command in your PATH, respectively. Please read our documentation for the details.
• Supported CUDA 12 (39c3538)
• Repaired C10 to C19 point groups (0c110f6, thanks to @huwjenkins)
• Fixed the CTF-premultiplication flag upon re-extraction (db5f635)
• Repaired implicit 3.0 to 3.1 STAR format conversion (042319e)
• Supported the latest CTFFIND (f6edba3)
• Fixed a memory issue (9908f51, thanks to @do-jason)

4.0.0

This is the first stable version of RELION 4.0. With the release of this version, earlier RELION versions (3.1.x) are no longer supported. We recommend all RELION users to upgrade to this version.

For the list of new features, please look at the "What's new?" page in our documentation and the following papers.

• "New tools for automated cryo-EM single-particle analysis in RELION-4.0" Biochem. J., 2021
• "A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0" bioRxiv, 2022

3.1.4

This is the final maintenance (bug fix) release from RELION 3.1.3. RELION 4.0 succeeds this release. We will no longer investigate and fix bugs in RELION 3.1.x.

The most important change since RELION 3.1.3 is that symmetry relaxation for non-cyclic point groups was blocked. This feature has been broken for non-cyclic point groups but earlier versions allowed the job to run, giving wrong results (see issue #796). The --helical_nstart option of relion_refine was also repaired (see #799).

In addition to these, various bugs (resource leaks, buffer overflows etc) were fixed and compatibility with newer compilers/environments was improved. See Git commit logs for the details.

3.1.3

This is a maintenance (bug fix) release from RELION 3.1.2. Everyone using RELION 3.1.2 or earlier should upgrade to this version. We will not investigate bug reports and questions on earlier versions.

Changes since RELION 3.1.2 include:

• Compatibility fix with CUDA 11.5 (by Alexey Romanenko)
• Compatibility fix with Intel oneAPI SDK (by Intel engineers)
  Please see installation manual to learn how to use Intel compilers. Do not use CC, CXX, MPICC, MPICXX environmental variables.
• Fix race conditions in local scratch (by Andreas Schenk)
• Fixed buffer overflow in FileName::compose (by Andreas Schenk)
• relion_convert_to_tiff: treat MODE 0 MRC as signed
• MotionCorr: treat pixels with zero gain as defects even in non-EER movies
• Bayesian Polish: fix defects in EER
• Gentle clean: remove duplicated code
• EER: prevent crash in corrupted EER files

3.1.2

This is a minor update from RELION 3.1.1. Everyone using RELION 3.1.1 or earlier should upgrade to this version. We will not investigate bug reports and questions on earlier versions.

Changes since RELION 3.1.1 include:

• We are migrating documentation from RELION wiki to ReadTheDocs.
• libtiff is no longer optional; it is necessary for compilation
• Switch to FFTW 3.3.8 from 3.3.4 (earlier versions are broken for GCC 8: http://www.fftw.org/release-notes.html)
• Support the AMD-optimized version of FFTW with the -DAMDFFTW ONoption in CMake
• 3DCTF: fix a bug reported by @dtegunov (#710)
• relion_image_handler: do not add image index to filenames in STAR file if an image file is not a stack (#705)
• CTFFIND wrapper: support (non-movie) TIFF images (#728, thanks to @gruchalla)
• GUI: do not add --sigma_rot, --sigma_tilt, --sigma_psi for local search in Refine3D
• Suppress warnings about private TIFF tags in EER (#735)
• Multibody: support SIDESPLITTER (please use the latest wrapper)
• Fix issues with undefined labels in STAR files (#641)
• Replace controversial technical terms regarding MPI (#739)

Unfortunately, there are several remaining issues to be fixed in later updates. Frequent problems include:

• Reboxing in a subtract job consumes a huge amount of RAM. This is actually a GLIBC, not RELION, issue. A workaround is described in #673.
• It might fail to compile with GCC and Intel MKL on some Linux distributions. A patch (58bffcb) is described in #731.

See https://github.com/3dem/relion/issues for details.

3.1.1

This is a minor update from RELION 3.1.0. Everyone using RELION 3.1.0 or earlier should upgrade to this version.

Changes since RELION 3.1.0 include:

• Supported the EER movie format for Falcon4.
  Please read https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Image_compression#Falcon4_EER carefully for detailed instructions.
• Changed defect correction to use a random pick from neighboring good pixels, instead of the average of them.
• Fixed --keep_ctfs_micrographs in Extract to respect the optics groups in the micrograph STAR file.
• Updated Gentle Clean to delete temporary files from CtfRefine.
• Merged optimizations for GPU (--gpu) and Intel CPUs (--cpu) contributed by NVIDIA and Intel engineers.

Unfortunately, there are several remaining issues to be fixed in later updates. Frequent problems are:

• SIDESPLITTER does not work with Multibody refinement.
• Use of undefined labels in STAR files causes problems with some components (e.g. Extract). #641
• Memory leak in Subtract job (could not be reproduced at LMB). #673

See https://github.com/3dem/relion/issues for details.