Owner

ccpem

6 indexed repositories · View on GitHub

mrcfile
A Python implementation of the MRC2014 file format

Python · 86 stars
affinity-vae
Self-supervised method for disentanglement, clustering and classification of objects in multidimensional image data

Python · 17 stars
empiarreader
Reader for EMPIAR datasets

Python · 14 stars
roodmus

Jupyter Notebook · 8 stars
profet
Protein structure Fetcher

Python · 6 stars
caked

Jupyter Notebook · 2 stars

Open All

82 open issues indexed

mx,my and mz potentially being set wrong Open

ccpem/mrcfile#23 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
bug: possibility of writing invalid headers yielding unreadable files Open

ccpem/mrcfile#51 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add option for mrcfile-header to print extended header when it has a known type Open

ccpem/mrcfile#55 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Writing/reading extended header seems to be broken in latest version Open

ccpem/mrcfile#58 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Make mrcfile.validate silent Open

ccpem/mrcfile#66 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Is there away to just append anew "slice"to an existing file. without loading all the existing data? Open

ccpem/mrcfile#67 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Better handling of signed bytes MRC files Open

ccpem/mrcfile#69 · 2 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Improve handling of header labels Open

ccpem/mrcfile#70 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Extended header in SERI format Open

ccpem/mrcfile#71 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Compatibility with NumPy 2.4 Open

ccpem/mrcfile#74 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
DeprecationWarning: setting header.dtype is deprecated in NumPy 2.5 Open

ccpem/mrcfile#75 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Particle distribution in micrographs Open

bug understanding Parakeet v0.3.0

ccpem/roodmus#7 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Look into cisTEM for micrograph simulation Open

enhancement wontfix

ccpem/roodmus#11 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Update plot formatting Open

v0.3.0

ccpem/roodmus#12 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
add CONTRIBUTING.md to repo Open

ccpem/roodmus#14 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
add .cff file (for easy citation) with doi to repo Open

ccpem/roodmus#15 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Refactor num_ugraphs to be implemented within analysis object. This resolves unnecessary matching of particles in all ugraphs in a metadata file. Open

enhancement v0.3.0

ccpem/roodmus#16 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 14, 2026
Add analysis tests for per-particle defoci and 1-to-1 matching labelling Open

ccpem/roodmus#17 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Generation of the simulated Gaussian random field (GRF) ice model Open

understanding Parakeet

ccpem/roodmus#19 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
CTF simulation Open

understanding Parakeet

ccpem/roodmus#21 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
MTF generation and e-/A^2/second dependence in implementation (also relation to DQE) Open

understanding Parakeet

ccpem/roodmus#22 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
inelastic scattering models Open

understanding Parakeet

ccpem/roodmus#23 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Parameters for noisy, radiation damaged, inelastic scattering-inclusive, fractionated dataset generation Open

ccpem/roodmus#26 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Roodmus v0.3.0 utilities Open

ccpem/roodmus#28 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
plot_ctf incorrect CTF Open

bug v0.3.0

ccpem/roodmus#31 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
integration test for heterogeneity module Open

enhancement v0.3.0

ccpem/roodmus#33 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Setup sphinx docs Open

documentation v0.3.0

ccpem/roodmus#35 · 2 comments · 0 reactions · 2 assignees · Indexed Sep 14, 2026
Sort out het_metrics.log file Open

enhancement v0.3.0

ccpem/roodmus#37 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Updating roodmus to use parakeet v0.6.X Open

ccpem/roodmus#44 · 17 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Improved parallelization with mpi Open

enhancement

ccpem/roodmus#45 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Non-uniform placement of particles in the virtual sample Open

enhancement

ccpem/roodmus#46 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
BIM model incompatible with atomic ice generation Open

bug v0.3.0

ccpem/roodmus#48 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
solvent noise model Open

ccpem/roodmus#51 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Check beam-induced motion model Open

ccpem/roodmus#52 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Ice thickness variation Open

enhancement

ccpem/roodmus#55 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Parakeet does not generate uniformly sampled poses Open

bug

ccpem/roodmus#56 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add other sources of PDB Open

ccpem/profet#10 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Parakeet support Open

ccpem/profet#41 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Can we move to an Apache v2 licence Open

ccpem/affinity-vae#7 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add a contributing guide Open

documentation good first issue

ccpem/affinity-vae#10 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add to pypi / make a conda package Open

ccpem/affinity-vae#11 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Update the method of metadata gathering from pandas to Cudf (cuda df) Open

priority

ccpem/affinity-vae#22 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add functions for calculating affinity matrix (both SOAP and FSC) Open

enhancement

ccpem/affinity-vae#32 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Prevent users from leaving a trailing comma at the end of the classes.csv file Open

good first issue priority

ccpem/affinity-vae#63 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
creating read the docs Open

bug

ccpem/affinity-vae#108 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Refactor evaluation during training (call function from eval rather than test_dir) Open

bug

ccpem/affinity-vae#115 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
strip spaces from the name of classes in affinity.csv or classes.csv Open

good first issue priority

ccpem/affinity-vae#156 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
remove white space from reconstruction plots Open

ccpem/affinity-vae#160 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
selection of encodings for pose and latent interpolation Open

ccpem/affinity-vae#236 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Consolidate embedding code Open

ccpem/affinity-vae#244 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

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