cellpose
latest
Basics:
Installation
GUI
Inputs
Settings
Outputs
Models
Image Restoration
Training
OpenVINO
FAQ
Examples:
In a notebook
Command line
Reference:
Cellpose API Guide
Cellpose CLI
cellpose
Index
Edit on GitHub
Index
_
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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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L
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M
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N
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O
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P
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R
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S
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T
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U
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W
_
__init__() (cellpose.models.CellposeModel method)
,
[1]
A
add_model() (in module cellpose.io)
aggregated_jaccard_index() (in module cellpose.metrics)
assign_device() (in module cellpose.core)
average_precision() (in module cellpose.metrics)
average_tiles() (in module cellpose.transforms)
B
batchconvstyle (class in cellpose.resnet_torch)
boundary_scores() (in module cellpose.metrics)
builtin (cellpose.models.CellposeModel attribute)
,
[1]
C
Cellpose (class in cellpose.models)
,
[1]
cellpose.core
module
cellpose.dynamics
module
cellpose.io
module
cellpose.metrics
module
cellpose.models
module
cellpose.plot
module
cellpose.resnet_torch
module
cellpose.train
module
cellpose.transforms
module
cellpose.utils
module
CellposeDenoiseModel (class in cellpose.denoise)
CellposeModel (class in cellpose.models)
,
[1]
check_mkl() (in module cellpose.core)
circleMask() (in module cellpose.utils)
compute_masks() (in module cellpose.dynamics)
concatenation (cellpose.resnet_torch.CPnet attribute)
conv_3D (cellpose.resnet_torch.CPnet attribute)
convert_image() (in module cellpose.transforms)
cp (cellpose.models.Cellpose attribute)
,
[1]
(cellpose.models.SizeModel attribute)
,
[1]
CPnet (class in cellpose.resnet_torch)
D
DenoiseModel (class in cellpose.denoise)
device (cellpose.models.Cellpose attribute)
,
[1]
(cellpose.models.CellposeModel attribute)
,
[1]
(cellpose.models.SizeModel attribute)
,
[1]
(cellpose.resnet_torch.CPnet property)
diam_labels (cellpose.models.CellposeModel attribute)
,
[1]
(cellpose.resnet_torch.CPnet attribute)
diam_mean (cellpose.denoise.DenoiseModel attribute)
(cellpose.models.Cellpose attribute)
,
[1]
(cellpose.models.CellposeModel attribute)
,
[1]
(cellpose.models.SizeModel attribute)
,
[1]
(cellpose.resnet_torch.CPnet attribute)
diameters() (in module cellpose.utils)
dilate_masks() (in module cellpose.utils)
disk() (in module cellpose.plot)
distance_to_boundary() (in module cellpose.utils)
download_url_to_file() (in module cellpose.utils)
downsample (cellpose.resnet_torch.CPnet attribute)
(class in cellpose.resnet_torch)
dx_to_circ() (in module cellpose.plot)
E
eval() (cellpose.denoise.CellposeDenoiseModel method)
(cellpose.denoise.DenoiseModel method)
(cellpose.models.Cellpose method)
,
[1]
(cellpose.models.CellposeModel method)
,
[1]
,
[2]
,
[3]
(cellpose.models.SizeModel method)
,
[1]
F
fill_holes_and_remove_small_masks() (in module cellpose.utils)
flow_error() (in module cellpose.metrics)
flush() (cellpose.utils.TqdmToLogger method)
follow_flows() (in module cellpose.dynamics)
forward() (cellpose.resnet_torch.CPnet method)
G
gaussian_kernel() (in module cellpose.transforms)
get_centers() (in module cellpose.dynamics)
get_image_files() (in module cellpose.io)
get_label_files() (in module cellpose.io)
get_mask_compactness() (in module cellpose.utils)
get_mask_perimeters() (in module cellpose.utils)
get_mask_stats() (in module cellpose.utils)
get_masks() (in module cellpose.dynamics)
get_masks_unet() (in module cellpose.utils)
get_outline_multi() (in module cellpose.utils)
get_perimeter() (in module cellpose.utils)
gpu (cellpose.models.Cellpose attribute)
,
[1]
I
image_to_rgb() (in module cellpose.plot)
imread() (in module cellpose.io)
imsave() (in module cellpose.io)
interesting_patch() (in module cellpose.plot)
L
labels_to_flows() (in module cellpose.dynamics)
load_images_labels() (in module cellpose.io)
load_model() (cellpose.resnet_torch.CPnet method)
load_train_test_data() (in module cellpose.io)
M
make_style (cellpose.resnet_torch.CPnet attribute)
(class in cellpose.resnet_torch)
make_tiles() (in module cellpose.transforms)
map_coordinates() (in module cellpose.dynamics)
mask_ious() (in module cellpose.metrics)
mask_overlay() (in module cellpose.plot)
mask_rgb() (in module cellpose.plot)
masks_flows_to_seg() (in module cellpose.io)
masks_to_edges() (in module cellpose.utils)
masks_to_flows() (in module cellpose.dynamics)
masks_to_flows_cpu() (in module cellpose.dynamics)
masks_to_flows_gpu() (in module cellpose.dynamics)
masks_to_flows_gpu_3d() (in module cellpose.dynamics)
masks_to_outlines() (in module cellpose.utils)
mkldnn (cellpose.models.CellposeModel attribute)
,
[1]
(cellpose.resnet_torch.CPnet attribute)
module
cellpose.core
cellpose.dynamics
cellpose.io
cellpose.metrics
cellpose.models
cellpose.plot
cellpose.resnet_torch
cellpose.train
cellpose.transforms
cellpose.utils
move_axis() (in module cellpose.transforms)
move_min_dim() (in module cellpose.transforms)
N
nbase (cellpose.models.CellposeModel attribute)
,
[1]
(cellpose.resnet_torch.CPnet attribute)
nchan (cellpose.denoise.DenoiseModel attribute)
(cellpose.models.CellposeModel attribute)
,
[1]
nclasses (cellpose.models.CellposeModel attribute)
,
[1]
net (cellpose.denoise.DenoiseModel attribute)
(cellpose.models.CellposeModel attribute)
,
[1]
net_chan2 (cellpose.denoise.DenoiseModel attribute)
net_type (cellpose.denoise.DenoiseModel attribute)
(cellpose.models.CellposeModel attribute)
,
[1]
normalize99() (in module cellpose.transforms)
normalize99_tile() (in module cellpose.transforms)
normalize_img() (in module cellpose.transforms)
nout (cellpose.resnet_torch.CPnet attribute)
O
outline_view() (in module cellpose.plot)
outlines_list() (in module cellpose.utils)
outlines_list_multi() (in module cellpose.utils)
outlines_list_single() (in module cellpose.utils)
output (cellpose.resnet_torch.CPnet attribute)
P
pad_image_ND() (in module cellpose.transforms)
pretrained_model (cellpose.denoise.DenoiseModel attribute)
(cellpose.models.CellposeModel attribute)
,
[1]
pretrained_size (cellpose.models.Cellpose attribute)
,
[1]
(cellpose.models.SizeModel attribute)
,
[1]
R
radius_distribution() (in module cellpose.utils)
random_rotate_and_resize() (in module cellpose.transforms)
remove_bad_flow_masks() (in module cellpose.dynamics)
remove_edge_masks() (in module cellpose.utils)
remove_model() (in module cellpose.io)
resdown (class in cellpose.resnet_torch)
reshape() (in module cellpose.transforms)
residual_on (cellpose.resnet_torch.CPnet attribute)
resize_and_compute_masks() (in module cellpose.dynamics)
resize_image() (in module cellpose.transforms)
resup (class in cellpose.resnet_torch)
run_3D() (in module cellpose.core)
run_net() (in module cellpose.core)
S
save_masks() (in module cellpose.io)
save_model() (cellpose.resnet_torch.CPnet method)
save_rois() (in module cellpose.io)
save_to_png() (in module cellpose.io)
show_segmentation() (in module cellpose.plot)
size_distribution() (in module cellpose.utils)
SizeModel (class in cellpose.models)
,
[1]
smooth_sharpen_img() (in module cellpose.transforms)
steps2D() (in module cellpose.dynamics)
steps2D_interp() (in module cellpose.dynamics)
steps3D() (in module cellpose.dynamics)
stitch3D() (in module cellpose.utils)
style_on (cellpose.resnet_torch.CPnet attribute)
sz (cellpose.models.Cellpose attribute)
,
[1]
(cellpose.resnet_torch.CPnet attribute)
T
TqdmToLogger (class in cellpose.utils)
train_seg() (in module cellpose.train)
train_size() (in module cellpose.train)
U
unaugment_tiles() (in module cellpose.transforms)
update_axis() (in module cellpose.transforms)
upsample (cellpose.resnet_torch.CPnet attribute)
(class in cellpose.resnet_torch)
use_gpu() (in module cellpose.core)
W
write() (cellpose.utils.TqdmToLogger method)
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