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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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Alternatives to calling micrograph names as argument list in topaz extract
#201
epkumpu
opened
6 days ago
1
Implement multi-GPU training for large datasets/tomograms
#200
DarnellGranberry
opened
3 weeks ago
0
Avoid loading entire dataset before training
#199
DarnellGranberry
opened
1 month ago
0
Allow for sampling micrographs/tomograms of different sizes
#198
DarnellGranberry
opened
1 month ago
0
Missing output flag in Topaz gui to train denoise model
#194
sven-lange
opened
3 months ago
7
Running Topaz on HPC got RuntimeError: cuDNN error: CUDNN_STATUS_EXECUTION_FAILED
#193
CFDavidHou
closed
2 months ago
2
Support long argument list specified as file for all topaz commands
#192
nfrasser
opened
4 months ago
2
ModuleNotFoundError: No module named 'pkg_resources'
#191
deepanshusachdeva5
opened
4 months ago
0
Radius for `topaz train`
#189
annwhoorma
closed
4 months ago
0
Add Intel PyTorch extension
#188
do-jason
opened
4 months ago
0
"score" in the output file
#187
ojasvijain
closed
2 months ago
0
Determining the downsampling factor & radius
#186
ojasvijain
closed
4 months ago
4
Preparing training data
#185
ojasvijain
closed
5 months ago
2
Training a denoising model on single exposure micrographs (no frames/movies), even possible?
#184
DennisDannecker
closed
2 months ago
6
Computing Metrics
#183
ojasvijain
closed
2 months ago
0
Running topaz denoise
#181
ojasvijain
closed
6 months ago
7
PyTorch confilct with NumPy
#179
chris-hypercag
closed
2 months ago
1
Fix #177 with a --version output containing only a semver string
#178
Guillawme
closed
2 months ago
0
Version string rejected by cryoSPARC
#177
Guillawme
closed
2 months ago
2
Fix typo in RandomImageTransforms
#176
kephale
closed
9 months ago
1
RuntimeError: Could not infer dtype of numpy.int64
#175
rdrighetto
closed
9 months ago
3
topaz convert: when image_name is numbers like "001", one error
#174
IAMCHF
closed
10 months ago
2
Topaz training error in multiprocessing data loader
#173
tbepler
opened
11 months ago
0
MRC library version incompatible
#171
BastiaanMM
closed
2 months ago
5
0.2.5 vs 0.2.5a
#169
jjv5
closed
10 months ago
1
from topaz.utils.data.loader import load_image ModuleNotFoundError: No module named 'topaz.utils'; 'topaz' is not a package
#168
Casion151
closed
2 months ago
1
Avoid pandas df.iterrows dtype conversion
#167
fullerjamesr
closed
1 year ago
1
topaz is not using gpu
#165
diffracteD
closed
1 year ago
7
Plot training metrics by default?
#164
Guillawme
opened
1 year ago
0
Singulairty container should be updated to 0.2.5
#163
eMKiso
closed
2 months ago
0
Topaz Train/Cross-Validation failed with AssertionError: Subprocess exited with status -9.
#160
PeterXTH
closed
2 months ago
1
CudaWarning: Found no NVIDIA driver on your system. Please check that you have an NVIDIA GPU and installed a driver from http://www.nvidia.com/Download/index.aspx
#154
pconesa
closed
1 year ago
3
ImportError: (...)/libmkldnn.so.0: undefined symbol: cblas_sgemm_alloc
#152
lucajovine
closed
1 year ago
1
How to Reproduce the Full Pretraining
#149
vzmath
closed
2 years ago
0
denoise training using tif format movie file
#148
ning-2022
closed
2 years ago
5
topaz denoise crashes with RuntimeError: CUDA out of memory
#145
maxxrenner
closed
2 years ago
4
Topaz filament picking
#144
sunny1226
opened
2 years ago
7
Git checkout errors
#143
bu-bgregor
closed
2 years ago
2
Create ci.yml
#141
DarnellGranberry
closed
2 years ago
0
Create ci.yml
#140
DarnellGranberry
closed
2 years ago
0
Importing particle star file to cryosparc
#138
sasriram
opened
2 years ago
0
Can denoising be applied in a particle-wise situation?
#137
zhaotf16
closed
2 years ago
1
training topaz demonising model with frames collected in .eer format
#125
samuelhaysom
closed
2 years ago
0
Topaz DeNoise3D and array size
#122
schmitbp
closed
2 years ago
10
TypeError using Topaz denoise
#119
bencreekm
closed
2 years ago
1
ERROR: no training particles specified.
#113
jianhaoc
closed
2 years ago
2
Is this method related to the commercial software Topaz DeNoise AI
#111
AAAeray
closed
3 years ago
0
particles format
#103
jianhaoc
closed
3 years ago
1
Issue: particles picked by Topaz are not displayed in Relion GUI
#102
UHeinemeyer
closed
3 years ago
4
Support mode 12 (float16) MRC files
#99
biochem-fan
closed
3 years ago
0
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