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tbepler
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topaz
Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.
GNU General Public License v3.0
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Support for Cuda 11
#98
alexjnoble
closed
3 years ago
1
Support MRC mode 12
#97
biochem-fan
closed
3 years ago
3
Update and re-order
#94
alexjnoble
closed
3 years ago
0
Update
#93
alexjnoble
closed
3 years ago
2
A problem with denoising.
#88
yushuv
closed
3 years ago
0
topaz extract should have an option to stay away from micrograph edges
#87
tbepler
opened
3 years ago
0
topaz 0.2.5 not available through shub, conda, or pip.
#86
ulloaa
closed
2 years ago
10
Allow topaz relion wrapper to detect sub-folders of movie files
#85
zruan
opened
3 years ago
1
Folder hierarchy not fully preserved for *_topazpicks.star
#84
zruan
opened
3 years ago
5
tag and release for v0.2.5
#81
jasonkey
closed
3 years ago
2
Singularity with Relion integration
#80
Jason-vR
opened
3 years ago
1
Fix MRC parsing bug when dtype is int16
#79
tbepler
closed
3 years ago
1
pkg_resources.DistributionNotFound: The 'dataclasses' distribution was not found and is required by torch
#77
werhoog
opened
3 years ago
4
Improve documentation
#76
Guillawme
opened
3 years ago
4
topaz insttaltion issue
#73
diffracteD
closed
3 years ago
3
Display number of picked particles in picking GUI
#72
Guillawme
opened
3 years ago
0
3D demonising and ctf correction
#71
samuelhaysom
closed
3 years ago
2
ImportError using topaz with python2.7
#69
sbliven
closed
3 years ago
4
NumPy array Warning
#68
girodat
opened
3 years ago
5
error when reading topaz denoise3d output
#67
ssscj
closed
3 years ago
10
Quality of denoising
#66
dgvjay
closed
3 years ago
10
v0.2.5 update
#65
alexjnoble
closed
3 years ago
0
RuntimeWarning: overflow encountered in exp in training
#64
huwjenkins
opened
3 years ago
2
Fix Dockerfile
#63
fixdocker
closed
3 years ago
2
Is there a way to decrease the restriction distance between predicted particles?
#62
Zivvvo
closed
3 years ago
2
Automatically create subdirectories when using 'topaz convert' to box files
#61
tbepler
opened
3 years ago
0
error when using topaz convert
#60
olibclarke
closed
3 years ago
11
Relion integration and some updates
#59
alexjnoble
closed
4 years ago
0
Add option for Gaussian filter of tomograms post denoising
#58
tbepler
closed
4 years ago
1
Cast tomograms to float32 when opened to prevent integer rounding errors
#57
tbepler
closed
4 years ago
1
Better RELION integration
#56
biochem-fan
opened
4 years ago
19
Error when resizing particles with topaz particle_stack
#55
TehNomad
closed
4 years ago
1
Installation problem and presence of Unet-3d-10a in v0.2.4
#54
dgvjay
closed
4 years ago
3
Updated Singularity and Docker files & minor cosmetic GUI update
#53
nysbc
closed
4 years ago
0
Update README.md
#52
alexjnoble
closed
4 years ago
0
Number of threads
#51
biochem-fan
closed
4 years ago
3
GPU memory usage for denoising
#50
Jason-vR
closed
4 years ago
3
"Integer overflow in ysize" when loading very large micrographs
#49
tbepler
closed
4 years ago
1
Model Training Failed
#48
chensongzh
closed
4 years ago
4
Input micrographs as file
#47
rfleiro
opened
4 years ago
4
problems with topaz test
#46
gmontoya-dk
closed
4 years ago
10
Topaz commands not running.
#45
ACheong97
closed
4 years ago
12
Add warning for when micrograph image names include the file extension
#44
tbepler
opened
4 years ago
0
Unrecognized arguments: --lowpass when using denoise
#43
Leosuziqi
closed
4 years ago
0
bug in running tutorial
#42
ajian-he
closed
4 years ago
16
Store trained model in models for denoise_image function
#41
JayJaewonYoo
closed
4 years ago
1
Question about cross-validation (choosing 'n' and number of epochs)
#40
3rdfloorTom
closed
4 years ago
3
Training on multi gpus
#39
nguyen14ck
closed
4 years ago
1
Updated the GUI to v0.2.2
#38
alexjnoble
closed
4 years ago
0
Add ETA indicator to topaz preprocess?
#37
olibclarke
closed
4 years ago
8
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