Topaz
latest
Contents:
Installation
Tutorials (coming soon)
Topaz Commands
Algorithms
Denoising
Methods
Metrics and Statistics
Models
Transformations
Utilities
Scripts
Use with RELION
Use with CryoSPARC
Topaz
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Index
Edit on GitHub
Index
A
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B
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C
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D
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E
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F
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G
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I
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K
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L
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M
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N
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
A
AffineDenoise (class in topaz.denoise)
AffineFilter (class in topaz.denoise)
alpha (topaz.mrc.MRCHeader attribute)
amax (topaz.mrc.MRCHeader attribute)
amean (topaz.mrc.MRCHeader attribute)
amin (topaz.mrc.MRCHeader attribute)
as_mask() (in module topaz.utils.picks)
autoencoder_loss() (in module topaz.methods)
average_precision() (in module topaz.metrics)
B
BasicConv (class in topaz.model.features.basic)
BasicConv2d (class in topaz.model.features.resnet)
beta (topaz.mrc.MRCHeader attribute)
boxes_to_coordinates() (in module topaz.utils.conversions)
,
[1]
C
cmap (topaz.mrc.MRCHeader attribute)
Conv127 (class in topaz.model.features.basic)
conv127() (in module topaz.model.factory)
conv31() (in module topaz.model.factory)
Conv63 (class in topaz.model.features.basic)
conv63() (in module topaz.model.factory)
ConvGenerator (class in topaz.model.generative)
coordinates_table_to_dict() (in module topaz.utils.data.coordinates)
coordinates_to_boxes() (in module topaz.utils.conversions)
,
[1]
coordinates_to_eman2_json() (in module topaz.utils.conversions)
,
[1]
coordinates_to_star() (in module topaz.utils.conversions)
,
[1]
correct_spatial_covariance() (in module topaz.denoise)
creatid (topaz.mrc.MRCHeader attribute)
D
denoise() (in module topaz.denoise)
denoise_patches() (in module topaz.denoise)
denoise_stack() (in module topaz.denoise)
DenoiseNet (class in topaz.denoise)
DenoiseNet2 (class in topaz.denoise)
DenseBlock (class in topaz.model.features.densenet)
(class in topaz.model.features.msnet)
DenseLayer (class in topaz.model.features.densenet)
(class in topaz.model.features.msnet)
DenseNet (class in topaz.model.features.densenet)
(class in topaz.model.features.msnet)
downsample() (in module topaz.utils.image)
E
enumerate_pn_coordinates() (in module topaz.utils.data.sampler)
enumerate_pu_coordinates() (in module topaz.utils.data.sampler)
estimate_unblur_filter() (in module topaz.denoise)
estimate_unblur_filter_gaussian() (in module topaz.denoise)
eval_mask_denoise() (in module topaz.denoise)
eval_noise2noise() (in module topaz.denoise)
F
fill() (topaz.model.classifier.LinearClassifier method)
(topaz.model.features.basic.BasicConv method)
(topaz.model.features.densenet.DenseNet method)
(topaz.model.features.msnet.DenseNet method)
(topaz.model.features.msnet.PyramidNet method)
(topaz.model.features.msnet.ResidMultiScaleNet method)
(topaz.model.features.msnet.RMSNet10 method)
(topaz.model.features.msnet.RMSNet7 method)
(topaz.model.features.resnet.BasicConv2d method)
(topaz.model.features.resnet.MaxPool method)
(topaz.model.features.resnet.ResidA method)
(topaz.model.features.resnet.ResNet method)
fit() (topaz.transform.scaled_gaussian_mixture.ScaledGaussianMixture method)
forward() (topaz.denoise.AffineDenoise method)
(topaz.denoise.AffineFilter method)
(topaz.denoise.DenoiseNet method)
(topaz.denoise.DenoiseNet2 method)
(topaz.denoise.GaussianDenoise method)
(topaz.denoise.GaussianDenoise3d method)
(topaz.denoise.Identity method)
(topaz.denoise.InvGaussianFilter method)
(topaz.denoise.UDenoiseNet method)
(topaz.denoise.UDenoiseNet2 method)
(topaz.denoise.UDenoiseNet3 method)
(topaz.denoise.UDenoiseNet3D method)
(topaz.denoise.UDenoiseNetSmall method)
(topaz.model.classifier.LinearClassifier method)
(topaz.model.features.basic.BasicConv method)
(topaz.model.features.densenet.DenseBlock method)
(topaz.model.features.densenet.DenseLayer method)
(topaz.model.features.densenet.DenseNet method)
(topaz.model.features.densenet.MultiscaleDenseNet method)
(topaz.model.features.msnet.DenseBlock method)
(topaz.model.features.msnet.DenseLayer method)
(topaz.model.features.msnet.DenseNet method)
(topaz.model.features.msnet.MultiscaleDenseNet method)
(topaz.model.features.msnet.PyramidNet method)
(topaz.model.features.msnet.ResidMultiScaleBlock method)
(topaz.model.features.msnet.ResidMultiScaleNet method)
(topaz.model.features.msnet.RMSNet10 method)
(topaz.model.features.msnet.RMSNet7 method)
(topaz.model.features.resnet.BasicConv2d method)
(topaz.model.features.resnet.MaxPool method)
(topaz.model.features.resnet.ResidA method)
(topaz.model.features.resnet.ResNet method)
(topaz.model.generative.ConvGenerator method)
G
gamma (topaz.mrc.MRCHeader attribute)
gaussian() (in module topaz.denoise)
gaussian3d() (in module topaz.denoise)
gaussian_filter() (in module topaz.denoise)
gaussian_filter_3d() (in module topaz.denoise)
GaussianDenoise (class in topaz.denoise)
GaussianDenoise3d (class in topaz.denoise)
GaussianNoise (class in topaz.denoise)
GE_binomial (class in topaz.methods)
GE_KL (class in topaz.methods)
get() (topaz.utils.data.loader.ImageDirectoryLoader method)
(topaz.utils.data.loader.ImageTree method)
get_feature_extractor() (in module topaz.model.factory)
get_mode() (in module topaz.mrc)
gmm_fit() (in module topaz.stats)
gmm_fit_numpy() (in module topaz.stats)
I
Identity (class in topaz.denoise)
idtype (topaz.mrc.MRCHeader attribute)
ImageDirectoryLoader (class in topaz.utils.data.loader)
ImageTree (class in topaz.utils.data.loader)
imodFlags (topaz.mrc.MRCHeader attribute)
imodStamp (topaz.mrc.MRCHeader attribute)
insize_from_outsize() (in module topaz.model.utils)
inverse_filter() (in module topaz.denoise)
InvGaussianFilter (class in topaz.denoise)
ispg (topaz.mrc.MRCHeader attribute)
K
kfold() (in module topaz.utils.data.partition)
L
L0Loss (class in topaz.denoise)
LabeledImageCropDataset (class in topaz.utils.data.loader)
LabeledRegionsDataset (class in topaz.utils.data.loader)
labels (topaz.mrc.MRCHeader attribute)
latent_dim (topaz.model.classifier.LinearClassifier property)
lens (topaz.mrc.MRCHeader attribute)
LinearClassifier (class in topaz.model.classifier)
load_image() (in module topaz.utils.data.loader)
(topaz.denoise.NoiseImages method)
(topaz.denoise.PairedImages method)
load_images_from_directory() (in module topaz.utils.data.loader)
load_images_from_list() (in module topaz.utils.data.loader)
load_jpeg() (in module topaz.utils.data.loader)
load_model() (in module topaz.denoise)
(in module topaz.model.factory)
load_mrc() (in module topaz.utils.data.loader)
load_pil() (in module topaz.utils.data.loader)
load_png() (in module topaz.utils.data.loader)
load_tiff() (in module topaz.utils.data.loader)
lowpass() (in module topaz.denoise)
lowpass3d() (in module topaz.denoise)
M
make_header() (in module topaz.mrc)
make_modules() (topaz.model.features.resnet.ResNet16 method)
(topaz.model.features.resnet.ResNet6 method)
(topaz.model.features.resnet.ResNet8 method)
mapc (topaz.mrc.MRCHeader attribute)
mapr (topaz.mrc.MRCHeader attribute)
maps (topaz.mrc.MRCHeader attribute)
match_coordinates() (in module topaz.algorithms)
match_coordinates_to_images() (in module topaz.utils.data.coordinates)
MaxPool (class in topaz.model.features.resnet)
mirror_y_axis() (in module topaz.utils.conversions)
,
[1]
mode (topaz.mrc.MRCHeader attribute)
module
topaz.algorithms
topaz.denoise
topaz.methods
topaz.metrics
topaz.model.factory
topaz.model.features.basic
topaz.model.features.densenet
topaz.model.features.msnet
topaz.model.features.resnet
topaz.model.generative
topaz.model.utils
topaz.mrc
topaz.stats
topaz.transform.scaled_gaussian_mixture
topaz.utils.conversions
,
[1]
topaz.utils.data.coordinates
topaz.utils.data.loader
topaz.utils.data.partition
topaz.utils.data.sampler
topaz.utils.image
topaz.utils.picks
topaz.utils.printing
topaz.utils.star
MRCHeader (class in topaz.mrc)
MultiscaleDenseNet (class in topaz.model.features.densenet)
(class in topaz.model.features.msnet)
mx (topaz.mrc.MRCHeader attribute)
my (topaz.mrc.MRCHeader attribute)
mz (topaz.mrc.MRCHeader attribute)
N
nd1 (topaz.mrc.MRCHeader attribute)
nd2 (topaz.mrc.MRCHeader attribute)
next (topaz.mrc.MRCHeader attribute)
next() (topaz.utils.data.sampler.ShuffledSampler method)
(topaz.utils.data.sampler.StratifiedCoordinateSampler method)
nint (topaz.mrc.MRCHeader attribute)
nlabl (topaz.mrc.MRCHeader attribute)
NoiseImages (class in topaz.denoise)
non_maximum_suppression() (in module topaz.algorithms)
non_maximum_suppression_3d() (in module topaz.algorithms)
norm_fit() (in module topaz.stats)
normalize() (in module topaz.stats)
nreal (topaz.mrc.MRCHeader attribute)
nx (topaz.mrc.MRCHeader attribute)
nxstart (topaz.mrc.MRCHeader attribute)
ny (topaz.mrc.MRCHeader attribute)
nystart (topaz.mrc.MRCHeader attribute)
nz (topaz.mrc.MRCHeader attribute)
nzstart (topaz.mrc.MRCHeader attribute)
P
PairedImages (class in topaz.denoise)
parse() (in module topaz.mrc)
(in module topaz.utils.star)
parse_star() (in module topaz.utils.star)
parse_star_body() (in module topaz.utils.star)
parse_star_loop() (in module topaz.utils.star)
PN (class in topaz.methods)
precision_recall_curve() (in module topaz.metrics)
PU (class in topaz.methods)
PyramidNet (class in topaz.model.features.msnet)
Q
quantize() (in module topaz.utils.image)
R
RandomImageTransforms (class in topaz.utils.data.sampler)
report() (in module topaz.utils.printing)
ResidA (class in topaz.model.features.resnet)
ResidMultiScaleBlock (class in topaz.model.features.msnet)
ResidMultiScaleNet (class in topaz.model.features.msnet)
ResNet (class in topaz.model.features.resnet)
ResNet16 (class in topaz.model.features.resnet)
ResNet6 (class in topaz.model.features.resnet)
ResNet8 (class in topaz.model.features.resnet)
rms (topaz.mrc.MRCHeader attribute)
RMSNet10 (class in topaz.model.features.msnet)
RMSNet7 (class in topaz.model.features.msnet)
S
save_image() (in module topaz.utils.image)
save_jpeg() (in module topaz.utils.image)
save_mrc() (in module topaz.utils.image)
save_png() (in module topaz.utils.image)
save_tiff() (in module topaz.utils.image)
ScaledGaussianMixture (class in topaz.transform.scaled_gaussian_mixture)
SegmentedImageDataset (class in topaz.utils.data.loader)
set_padding() (topaz.model.features.resnet.BasicConv2d method)
(topaz.model.features.resnet.MaxPool method)
(topaz.model.features.resnet.ResidA method)
(topaz.model.features.resnet.ResNet method)
ShuffledSampler (class in topaz.utils.data.sampler)
spatial_covariance() (in module topaz.denoise)
spatial_covariance_old() (in module topaz.denoise)
stamp (topaz.mrc.MRCHeader attribute)
step() (topaz.methods.GE_binomial method)
(topaz.methods.GE_KL method)
(topaz.methods.PN method)
(topaz.methods.PU method)
StratifiedCoordinateSampler (class in topaz.utils.data.sampler)
stratify() (in module topaz.utils.data.partition)
T
tilt_cx (topaz.mrc.MRCHeader attribute)
tilt_cy (topaz.mrc.MRCHeader attribute)
tilt_cz (topaz.mrc.MRCHeader attribute)
tilt_ox (topaz.mrc.MRCHeader attribute)
tilt_oy (topaz.mrc.MRCHeader attribute)
tilt_oz (topaz.mrc.MRCHeader attribute)
topaz.algorithms
module
topaz.denoise
module
topaz.methods
module
topaz.metrics
module
topaz.model.factory
module
topaz.model.features.basic
module
topaz.model.features.densenet
module
topaz.model.features.msnet
module
topaz.model.features.resnet
module
topaz.model.generative
module
topaz.model.utils
module
topaz.mrc
module
topaz.stats
module
topaz.transform.scaled_gaussian_mixture
module
topaz.utils.conversions
module
,
[1]
topaz.utils.data.coordinates
module
topaz.utils.data.loader
module
topaz.utils.data.partition
module
topaz.utils.data.sampler
module
topaz.utils.image
module
topaz.utils.picks
module
topaz.utils.printing
module
topaz.utils.star
module
train_mask_denoise() (in module topaz.denoise)
train_noise2noise() (in module topaz.denoise)
training (topaz.denoise.AffineDenoise attribute)
(topaz.denoise.AffineFilter attribute)
(topaz.denoise.DenoiseNet attribute)
(topaz.denoise.DenoiseNet2 attribute)
(topaz.denoise.GaussianDenoise attribute)
(topaz.denoise.GaussianDenoise3d attribute)
(topaz.denoise.Identity attribute)
(topaz.denoise.InvGaussianFilter attribute)
(topaz.denoise.UDenoiseNet attribute)
(topaz.denoise.UDenoiseNet2 attribute)
(topaz.denoise.UDenoiseNet3 attribute)
(topaz.denoise.UDenoiseNet3D attribute)
(topaz.denoise.UDenoiseNetSmall attribute)
(topaz.model.classifier.LinearClassifier attribute)
(topaz.model.features.basic.BasicConv attribute)
(topaz.model.features.basic.Conv127 attribute)
(topaz.model.features.basic.Conv63 attribute)
(topaz.model.features.densenet.DenseBlock attribute)
(topaz.model.features.densenet.DenseNet attribute)
(topaz.model.features.densenet.MultiscaleDenseNet attribute)
(topaz.model.features.msnet.DenseBlock attribute)
(topaz.model.features.msnet.DenseNet attribute)
(topaz.model.features.msnet.MultiscaleDenseNet attribute)
(topaz.model.features.msnet.PyramidNet attribute)
(topaz.model.features.msnet.ResidMultiScaleBlock attribute)
(topaz.model.features.msnet.ResidMultiScaleNet attribute)
(topaz.model.features.msnet.RMSNet10 attribute)
(topaz.model.features.msnet.RMSNet7 attribute)
(topaz.model.features.resnet.BasicConv2d attribute)
(topaz.model.features.resnet.MaxPool attribute)
(topaz.model.features.resnet.ResidA attribute)
(topaz.model.features.resnet.ResNet attribute)
(topaz.model.features.resnet.ResNet16 attribute)
(topaz.model.features.resnet.ResNet6 attribute)
(topaz.model.features.resnet.ResNet8 attribute)
(topaz.model.generative.ConvGenerator attribute)
transform() (topaz.transform.scaled_gaussian_mixture.ScaledGaussianMixture method)
U
UDenoiseNet (class in topaz.denoise)
UDenoiseNet2 (class in topaz.denoise)
UDenoiseNet3 (class in topaz.denoise)
UDenoiseNet3D (class in topaz.denoise)
UDenoiseNetSmall (class in topaz.denoise)
unfill() (topaz.model.classifier.LinearClassifier method)
(topaz.model.features.basic.BasicConv method)
(topaz.model.features.densenet.DenseNet method)
(topaz.model.features.msnet.DenseNet method)
(topaz.model.features.msnet.PyramidNet method)
(topaz.model.features.msnet.ResidMultiScaleNet method)
(topaz.model.features.msnet.RMSNet10 method)
(topaz.model.features.msnet.RMSNet7 method)
(topaz.model.features.resnet.BasicConv2d method)
(topaz.model.features.resnet.MaxPool method)
(topaz.model.features.resnet.ResidA method)
(topaz.model.features.resnet.ResNet method)
unquantize() (in module topaz.utils.image)
V
vd1 (topaz.mrc.MRCHeader attribute)
vd2 (topaz.mrc.MRCHeader attribute)
W
width (topaz.model.classifier.LinearClassifier property)
write() (in module topaz.mrc)
(in module topaz.utils.star)
X
xlen (topaz.mrc.MRCHeader attribute)
xorg (topaz.mrc.MRCHeader attribute)
Y
ylen (topaz.mrc.MRCHeader attribute)
yorg (topaz.mrc.MRCHeader attribute)
Z
zlen (topaz.mrc.MRCHeader attribute)
zorg (topaz.mrc.MRCHeader attribute)
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