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Ver5.1 - #1372

Merged

scheres merged 230 commits into

masterfrom

ver5.1

Sep 29, 2026

Merged

Ver5.1#1372
scheres merged 230 commits into
masterfrom
ver5.1

Commits on Nov 21, 2024
- added new functionality for autopicking amyloids, not optimal yet...
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  c8315f6
Commits on Nov 22, 2024
- updated find_amyloid
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  cc245d7
Commits on Nov 26, 2024
Commits on Nov 27, 2024
- repaired some minor issues
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  aa1ff59
- histograms of skewness and kurtosis
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  85c81f6
- add option to pick filaments as lines
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  dc262f6
- added option to extract helices from drawn lines
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  c7ba4c3
- display lines as lines
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  8659834
- continue with filament_type in lines mode and have red-coloured fom colouring
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  44297f4
Commits on Nov 28, 2024
- added colouring of manualpicker according to a FOM image
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  03124a2
- fix coulour scheme with fom images
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  bd8a326
- for David Barford: write out subtomos
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  ef62564
- repiared bug in subtomo when first tomogram is empty
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  8219dd0
Commits on Dec 2, 2024
- Merge branch 'amypick' into subtomo-relion3
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Commits on Dec 3, 2024
Commits on Dec 6, 2024
- better comment on why ysize for Fstmulti check
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  a850d8c
- allow setting individual pixel values in images
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  497cb32
- added option to output FFT power image
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  1d3da22
- also order tables on pre-exposure before generating the single MD
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  9d29660
- make sure the tomogram size gets sets correctly...
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  aa9e745
- option to skip wiener filter in fourier method for reconstruct tomograms
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  27d1602
- option to write out real subtomograms
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  487658e
- removed unnecessary check
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  05aba22
Commits on Dec 10, 2024
Commits on Dec 11, 2024
- rearrange subtomo
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  9a71c66
- tidied up code a bit
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  46ac332
- repaired bug reproject subtomos
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  e93f5ad
- Merge branch 'master' into subtomo-relion3
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  cd38280
- removed a big from fourier inversion tomogram reconstruction
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  aa2cf64
- replaced CTF-corrected SNR algorithm with much faster vector version
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  c263166
Commits on Dec 12, 2024
- repaired bug reported by Tina Drobnic in particle_reposition
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Commits on Dec 18, 2024
- set angpix in fom image header
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  e085769
- changed logic of tomogram reconstruction and subtomo extraction on the GUI, plus other changes to both programs...
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  56849b1
Commits on Dec 19, 2024
- allow empty isVisible and look for ytilt, not nominal tilt
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  5602833
- keep debugging for real_subtomos
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  8c73e47
- dont allow ignoring CTF until first peak for tomography
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  0361793
- dont always add --ctf to tomogram reconstruction
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  7b39885
- repiared bug in normalisation proj2d.mrcs
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  a96e1c9
Commits on Dec 20, 2024
Commits on Jan 14, 2025
- removed suprious debugging statement
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  b101bd6
- allow toggling of FOM-coluring and greyscale image
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  c169b1e
- sleep one second to prevent nervous toggling on a mac for fom-colouring
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  039b984
- put error message back for particles outside micrograph, and check this exception when using recenter
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  e3baaba
- resolve silly merge conflicts when merging in master
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  cdaba10
- fixed another merge error
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  598cd62
- moved version to devel
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  ffdef91
- Merge branch 'master' into ver5.1
  scheres
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  b44896e
- deactive tilt angle offset for continue jobs, as changing this half-way through will lead to errors in the star files
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  8fb2fda
- Merge branch 'master' into ver5.1
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  ad0533a
- made Jans extraction work again
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  cc3e941
Commits on Jan 15, 2025
- repaired bug in removal of decentered particles outside micrograph
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  c35c1e2
Commits on Jan 20, 2025
- Merge branch 'master' into ver5.1
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  a9d2aa5
Commits on Jan 22, 2025
- added non-signal for getting rid of ice crystals
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Commits on Jan 27, 2025
- give more info about z_perc errors
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Commits on Feb 5, 2025
- added same filament tracing code to find_amyloid as was present in modified topaz, with tweaking of some internal, hardcoded parameters
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  5ee8ea0
- make sure schemegui uses python from relion-5.0 conda environment
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  ad217b2
Commits on Feb 6, 2025
- dont retrace already traced micrographs in amyloid_finder, and deal with empty micrographs
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  2e8888b
- repaired bug in logfile plot generation
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  61854e0
Commits on Feb 11, 2025
- added local symmetry expansion
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  dcbae9c
- default psistep in find_amyloid to 5 degrees to prevent picking ice; also grow mask for nonsignal
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  9fc6071
Commits on Feb 13, 2025
- Jenny's new pi 🥳
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  e5a8b7b
- removed lightning dependency
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Commits on Feb 20, 2025
Commits on Feb 27, 2025
- added forgotton option to set only_do_unfinished
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- added option to read in specific blush model
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  e20029e
Commits on Mar 11, 2025
- Richards suggestion to calculate ice ring density relative to backgroun
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  4b825c7
- Merge branch 'master' into ver5.1
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  4e35c24
Commits on Mar 12, 2025
- reverted back from Richard's to Rafa's way of calculating ice ring
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  ee511de
- Merge branch 'ver5.1' into ver5.1-jenny-amyloid-picker
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  7e9344a
Commits on Mar 19, 2025
- take tomo-subtomo priors into account
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  06e1652
- add option --keep_priors_fixed to deal with priors in subtomogram averaging
  scheres
  committed
  9c3e5f9
- add Z-score for ice-ring calculation
  scheres
  committed
  853a238
- take tomo-subtomo priors into account
  scheres
  committed
  a9215de
- add option --keep_priors_fixed to deal with priors in subtomogram averaging
  scheres
  committed
  02cd848
- add Z-score for ice-ring calculation
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  a552487
Commits on Mar 20, 2025
- use kurtosis for icering density, but only if MotionCorr had calculated power spectrum, otherwise fall back on Rafa's method
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  07740b1
Commits on Mar 21, 2025
- implemented icepowerfraction and icekurtosis
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  532bd43
Commits on Mar 24, 2025
- debugged and changed Jennys segmentation and made everything work from GUI
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  130f6a6
- further optimisation of Jennys code and interaction with mine
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  dd30881
Commits on Mar 25, 2025
- remove too-close start-end points of filaments
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  eea0505
- resolved conflict when merging in jennys picker
  scheres
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  3432f3e
- only run extra ice stats when asked for with --extra_ice_stats option
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  76bbb44
- only run extra ice stats when asked for with --extra_ice_stats option, insert error
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  73e2718
- only run extra ice stats when asked for with --extra_ice_stats option, insert error2
  scheres
  committed
  e7430d4
- only run extra ice stats when asked for with --extra_ice_stats option, insert error3
  scheres
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  65db694
- Merge branch 'ver5.0'
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  6611b56
- no deviceInitilaise if we dont have CUDA
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  ce7fc0f
- no deviceInitilaise if we dont have CUDA
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  5c2fe97
- skip tracing is no GPUs
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  2e622db
- still more deviceInitialise in find_amyloid
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  a1db1b0
Commits on Mar 27, 2025
- touch empty star files if no filaments are picked, so not always repicking empty micrographs when continuing an old run
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  bbbf730
Commits on Apr 1, 2025
- warn instead of die if filament with a single point; TODO: remove this again after fixing Jenny's script!
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  fffa828
Commits on Apr 8, 2025
- Merge branch 'ver5.0' into devel-master
  biochem-fan
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  be6c658
Commits on Apr 11, 2025
- Replaced CUB with that distributed by the CUDA toolkit.
  dkimanius
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  683226a
- added weights in local symmetry averaging
  scheres
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  e99eccb
Commits on Apr 29, 2025
- repiared bad return call for empty micrographs
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  d791ff2
- put default model_path to /public/EM for now
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  2cd5457
Commits on May 1, 2025
- added option to skip tracing in find_amyloids
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  e83ba72
- allow tracing of amyloids on cpu too
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  13d7f42
- remove spurious cerr message
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  4e0b738
- explicitly define thread number in pytorch on cpu
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  fb99d1c
Commits on May 6, 2025
- only do 90-degree rotations: 90-180 is calculated from -y,x swaps
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  f04ef90
Commits on May 14, 2025
- perform amyloid autopick FOM and trace calculations separately, also do tracing over entire star files to prevent loading model each time
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  294eee5
Commits on May 21, 2025
- updated with picking lines, startend and partcles defined in autopick.star files, also updates to jenny's script
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  f183f03
Commits on May 22, 2025
- Compile model, bfloat16 for cuda
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  1ac0587
- Small optimisations
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  662ea7c
- by default do not know polarity of filaments
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  4e9483f
- for amyprep and amyproc schemes
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  6c45e9f
Commits on May 27, 2025
- repaired bug in setting picktype
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  b365bd5
- repaired bug in setting picktype
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  b04051b
Commits on May 28, 2025
- code suggestion Kent Thurber
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  c520fcc
- This implements pull request #1267 from 3dem/relion by Leandro Estrozi
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  d1c245f
Commits on May 30, 2025
- put nstart on gui for local averaging
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  8e5128a
Commits on Jun 3, 2025
- forgot only_unfinished for tracing of amyloids#
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  8267c25
Commits on Jun 4, 2025
Commits on Jun 5, 2025
- dont do init blobs for helical 2D classification
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  77c39a3
- removed again option to switch off rot prior updates
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  0c2010f
Commits on Jun 6, 2025
- dont die on broken micrographs
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  ede0761
- also write class_averages.star when selecting from Davids filament selection tool
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  9ff2c4f
Commits on Jun 9, 2025
- further tweaks to autopicker for amyloids
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  8dd93fb
- by default switch off GPU tracing of amyloids
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  c0db6e1
- more GUI tweaks to GPU tracing of amyloids
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  4414e86
Commits on Jun 11, 2025
- output downscaled fom and psi images
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  ae0cd9c
Commits on Jun 16, 2025
- better error handling
  scheres
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  a6ed141
- try going back to wider sigma2rot as Sofia reported problems with new version
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  bce6853
- also gigms2rot in mpi version
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  5a49fc4
Commits on Jun 19, 2025
- patch from nvidia to allow compilation with cuda13
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  6e29463
Commits on Jun 20, 2025
- make dependence on c++17 explicit
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Commits on Jun 23, 2025
- implemented option to paint masks in 2D images
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  88752b1
Commits on Jun 24, 2025
- made amypicker2 work
  scheres
  committed
  1e5e574
- further tweaks to paint_mask in relion_display
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  d2d1fc2
- now add_paint works ok
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  26f66ea
Commits on Jun 26, 2025
- Merge branch 'ver5.0' into ver5.1
  biochem-fan
  committed
  ade24f5
Commits on Jul 2, 2025
- added carbon detection to amyloid tracing
  scheres
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  35adad1
- added amyprep and amyproc Schemes
  scheres
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  dae2984
- try copying standard Scheme from relion scripts directory if it doesn't exist
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  committed
  e128777
Commits on Jul 8, 2025
- Bugfix in subtomo to SPA expansion
  dkimanius
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  9d001db
- relion_project overwrite flag
  dkimanius
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  de08e7d
Commits on Jul 15, 2025
- clarified output better
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  b4a616f
Commits on Jul 16, 2025
- introduce threshold on psi-jumps in tracing of amyloids
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  27178ab
- further changes to psi-angle tracing and defaults on gui for amyloid tracing
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  6fda976
Commits on Sep 5, 2025
- Merge branch 'devel-ver5.0' into devel-master
  biochem-fan
  committed
  5dee147
- Merge branch 'devel-ver5.0' into devel-master
  biochem-fan
  committed
  dc65e09
- Merge branch 'devel-master' into devel-ver5.1
  biochem-fan
  committed
  5ac49a2
- Merge branch 'devel-ver5.0' into devel-master
  biochem-fan
  committed
  829b720
- Merge branch 'devel-master' into devel-ver5.1
  biochem-fan
  committed
  b95ff9e
Commits on Sep 17, 2025
- fix rounding of box size when Fourier cropping image stacks in FourierCrop_fftwHalfStack
  bogdantoader
  committed
  b918cf2
Commits on Sep 19, 2025
Commits on Oct 17, 2025
- FindCUDA is removed in newer CMake versions (GitHub issue #1016, #1161,
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  1e2c625
Commits on Oct 20, 2025
- CMake: improved NVCC discovery and set C/C++ standards and CUDA_ARCH
  biochem-fan
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  19785d7
Commits on Oct 21, 2025
- CMake: properly set NVCC flags
  biochem-fan
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  2d9c9e9
- Merge branch 'ver5.0' into cmake_no_findCUDA
  biochem-fan
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  c900cf4
- Merge branch 'cmake_no_findCUDA' into ver5.1
  biochem-fan
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Commits on Nov 11, 2025
- implemented min/max for ice rings for Yue Zhang
  scheres
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  d97c63b
- Merge branch 'ver5.1' of https://github.com/3dem/relion-devel into ver5.1
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  720dfb3
Commits on Nov 12, 2025
- At the moment, build fails with CMake <= 3.20.
  biochem-fan
  committed
  41451e6
- Merge branch 'ver5.0' into cmake_no_findCUDA
  biochem-fan
  committed
  c820683
- Merge branch 'cmake_no_findCUDA' into ver5.1
  biochem-fan
  committed
  06357d9
- Merge branch 'ver5.1' of github.com:3dem/relion-devel into ver5.1
  biochem-fan
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  52aa481
Commits on Dec 15, 2025
- Merge branch 'master' of https://github.com/3dem/relion-devel
  scheres
  committed
  62d0900
- Merge branch 'master' into ver5.1
  scheres
  committed
  3f8c1eb
- Merge branch 'ver5.1' of https://github.com/3dem/relion-devel into ver5.1
  scheres
  committed
  aca3f2d
- add downloading of amyblush, amy-v1.0 weights
  scheres
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  80ffe18
- added amyblush on GUI, and format os subtomos as a dropdown menu
  scheres
  committed
  603bc58
- repaired small bug in blush versions
  scheres
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  4d79820
Commits on Dec 16, 2025
- deal with amyloid picker weights
  scheres
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  f09dd59
- debugging fetching weights for amypicker
  scheres
  committed
  86b939f
- import specific libraries later, so can re-use script for fetching weights too
  scheres
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  2fb54a4
- import specific libraries later, so can re-use script for fetching weights too
  scheres
  committed
  2b65918
- set version to 5.1.0
  scheres
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  e8e0e4c
- hmmm, getting trouble with local definitions of imports
  scheres
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  e93d257
- repaired indentation
  scheres
  committed
  df8c560
- go back to imports at the beginning
  scheres
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  d168c02
- only do carbon when asked for
  scheres
  committed
  2bf85d1
- write PNGs instead of plotting to screen for trace amyloids
  scheres
  committed
  81aa7f6
Commits on Dec 17, 2025
- changed buttons to teal colour for relion-5.1
  scheres
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  144b7d1
Commits on Jan 2, 2026
Commits on Jan 5, 2026
- added option to set tilt prior for helical extract jobs
  scheres
  committed
  695f3f0
- repaired bug tilt prior on gui
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  966c1d2
Commits on Jan 7, 2026
- use pytorh 2.9 in relion conda environment to use RTX50xx and Blackwell GPUs
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  1ea7378
- shorter name in titlebar of main gui
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  4a95745
Commits on Jan 8, 2026
Commits on Feb 3, 2026
- new text for background dynein structure
  scheres
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  6851215
- repair bug fourfilter
  scheres
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  9d94289
- remove skip_direction2 from helical orientations
  scheres
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  b07a33d
- allow tilted images for helices to set tilt prior
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  0332f23
Commits on Feb 6, 2026
- default tilt angle should be zero
  scheres
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  501c2be
Commits on Feb 12, 2026
- add option to search tilt in CTFFINF4.1; not exposed on GUI as doesn't allow power spectra precalculation, nor float16
  scheres
  committed
  9db40ec
Commits on Feb 18, 2026
- removed incorrect handling of tilted images for filaments
  scheres
  committed
  a74afde
- Merge branch 'master' of https://github.com/3dem/relion
  scheres
  committed
  cb26836
Commits on Mar 13, 2026
- Merge remote-tracking branch 'origin/master' into ver5.1
  biochem-fan
  committed
  50c5c5b
- Merge branch 'ver5.1' of github.com:3dem/relion-devel into ver5.1
  biochem-fan
  committed
  fcd6966
Commits on Mar 18, 2026
- Merge branch 'ver5.0' into ver5.1
  biochem-fan
  committed
  152c14a
- Remove Jasenko's experimental programs.
  biochem-fan
  committed
  9657685
Commits on Mar 25, 2026
- Pin napari-threedee and psygnal to working versions from relion-5.0 environment
  bogdantoader
  committed
  13cc231
Commits on Apr 1, 2026
- Fix amyloid tracer model download during `cmake` (Issue #1338).
  biochem-fan
  committed
  ed374e8
- Merge branch 'ver5.1' of github.com:3dem/relion-devel into ver5.1
  biochem-fan
  committed
  45f0a30
Commits on May 31, 2026
- Treat ".gain" gain references as TIFF on the generic image path (#1346)
  amineuron
  authored
  fe13611
Commits on Jul 18, 2026
- Merge branch 'ver5.0' into ver5.1
  biochem-fan
  committed
  15bc134
- Merge branch 'ver5.1' of github.com:3dem/relion into ver5.1
  biochem-fan
  committed
  04b3dc8
Commits on Aug 4, 2026
- --maskedge: clarify the default (as pointed out in #1349).
  biochem-fan
  committed
  260c6d2
Commits on Aug 16, 2026
- Merge branch 'ver5.0' into ver5.1
  biochem-fan
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  66ad085
Commits on Aug 19, 2026
- Merge branch 'ver5.0' into ver5.1
  biochem-fan
  committed
  d61cfdc
Commits on Aug 21, 2026
- Claude optimisation to reduce memory footprint and speed up
  scheres
  committed
  ad64784
- Merge branch 'ver5.1' of https://github.com/3dem/relion-devel into ver5.1
  scheres
  committed
  d6ba9c9
Commits on Aug 24, 2026
- mpi broadcast full per body rot+trans accuracy vectors
  fullerjamesr
  committed
  7e5af22
Commits on Sep 16, 2026
- Reuse exactly-sized free blocks in the custom GPU allocator (issue #1225) (#1369)
  arcusbuilds
  authored
  95017d2
- Merge branch 'ver5.1' of github.com:3dem/relion into ver5.1
  biochem-fan
  committed
  ad0b230
Commits on Sep 29, 2026
- Merge pull request #1362 from fullerjamesr/fix-multibody-accuracies-bcast
  scheres
  authored
  7f45a71
- Merge pull request #1371 from 3dem/ver5.0
  scheres
  authored
  108ef3c

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