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B

batchSize - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
batchSize(int) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Defines the batch size for training
build() - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Create a Cellpose2D, all ready for detection.
builder(File) - Static method in class qupath.ext.biop.cellpose.Cellpose2D
Load a previouslt serialized builder.
builder(String) - Static method in class qupath.ext.biop.cellpose.Cellpose2D
Create a builder to customize detection parameters.

C

cellConstrainScale - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
cellConstrainScale(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Constrain any cell expansion defined using CellposeBuilder.cellExpansion(double) based upon the nucleus size.
cellExpansion - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
cellExpansion(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Amount by which to expand detected nuclei to approximate the cell area.
CELLPOSE - qupath.ext.biop.cellpose.CellposeSetup.CellposeVersion
 
Cellpose2D - Class in qupath.ext.biop.cellpose
Dense object detection based on the following publication and code
Cellpose2D() - Constructor for class qupath.ext.biop.cellpose.Cellpose2D
 
CellposeBuilder - Class in qupath.ext.biop.cellpose
This class will contain all parameters that are usable by cellpose
cellposeChannels(int, int) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Sets the channels to use by cellpose, in case there is an issue with the order or the number of exported channels
CellposeExtension - Class in qupath.ext.biop.cellpose
Install Cellpose as an extension.
CellposeExtension() - Constructor for class qupath.ext.biop.cellpose.CellposeExtension
 
cellposeSetup - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
CellposeSetup - Class in qupath.ext.biop.cellpose
 
CellposeSetup() - Constructor for class qupath.ext.biop.cellpose.CellposeSetup
 
CellposeSetup.CellposeVersion - Enum in qupath.ext.biop.cellpose
 
channel1 - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
channel2 - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
channels(int...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Specify channels.
channels(String...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Specify channels by name.
channels(ColorTransforms.ColorTransform...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Define the channels (or color transformers) to apply to the input image.
classify(String) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Request that a classification is applied to all created objects.
classify(PathClass) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Request that a classification is applied to all created objects.
clusterDBSCAN() - Method in class qupath.ext.biop.cellpose.CellposeBuilder
DBSCAN clustering.
compartments - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
compartments(ObjectMeasurements.Compartments...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Specify the compartments within which intensity measurements are made.
CONDA - qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
 
constrainToParent - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
constrainToParent(boolean) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
If true, constrain nuclei and cells to any parent annotation (default is true).
createAnnotations() - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Create annotations rather than detections (the default).
creatorFun - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 

D

detectObjects(ImageData<BufferedImage>, Collection<? extends PathObject>) - Method in class qupath.ext.biop.cellpose.Cellpose2D
Detect cells within one or more parent objects, firing update events upon completion.
diameter - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
diameter(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
The extimated diameter of the objects to detect.
doCluster - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 

E

epochs(int) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Defines the number of epochs for training
excludeEdges - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
excludeEdges() - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Exclude on edges.

F

flowThreshold - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
flowThreshold(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Flow threshold to apply for detection, between 0 and 1.

G

getDescription() - Method in class qupath.ext.biop.cellpose.CellposeExtension
 
getDescription() - Method in enum qupath.ext.biop.cellpose.CellposeSetup.CellposeVersion
 
getDescription() - Method in enum qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
 
getEnvironmentNameOrPath() - Method in class qupath.ext.biop.cellpose.CellposeSetup
 
getEnvironmentType() - Method in class qupath.ext.biop.cellpose.CellposeSetup
 
getInstance() - Static method in class qupath.ext.biop.cellpose.CellposeSetup
 
getName() - Method in class qupath.ext.biop.cellpose.CellposeExtension
 
getQuPathVersion() - Method in class qupath.ext.biop.cellpose.CellposeExtension
 
getRepository() - Method in class qupath.ext.biop.cellpose.CellposeExtension
 
getVersion() - Method in class qupath.ext.biop.cellpose.CellposeExtension
 
getVersion() - Method in class qupath.ext.biop.cellpose.CellposeSetup
 
globalPathClass - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 

I

ignoreCellOverlaps - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
ignoreCellOverlaps(boolean) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
If true, ignore overlaps when computing cell expansion.
inputAdd(double...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Add an offset as a preprocessing step.
inputScale(double...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Multiply by a scale factor as a preprocessing step.
installExtension(QuPathGUI) - Method in class qupath.ext.biop.cellpose.CellposeExtension
 
invert - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
invert() - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Inverts the image channels within cellpose.
iou(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Select the Intersection over Union (IoU) cutoff for excluding overlapping detections.
iouThreshold - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 

L

learningRate - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
learningRate(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Defines the learning rate

M

maskThreshold - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
maskThreshold(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Probability threshold to apply for detection, between 0 and 1.
measureIntensity() - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Request default intensity measurements are made for all available cell compartments.
measureIntensity(Collection<ObjectMeasurements.Measurements>) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Request specified intensity measurements are made for all available cell compartments.
measurements - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
measureShape - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
measureShape() - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Request shape measurements are made for the detected cell or nucleus.
model - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
modelDirectory - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
modelDirectory(File) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Define the directory where the newly trained model should be saved

N

nEpochs - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
normalizePercentiles(double, double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Apply percentile normalization to the input image channels.

O

OMNIPOSE - qupath.ext.biop.cellpose.CellposeSetup.CellposeVersion
 
op - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
OTHER - qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
 
overlap - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 

P

pixelSize - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
pixelSize(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Resolution at which the cell detection should be run.
preprocess(ImageOp...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Add preprocessing operations, if required.

Q

qupath.ext.biop.cellpose - package qupath.ext.biop.cellpose
 
qupath.ext.biop.cmd - package qupath.ext.biop.cmd
 

R

runCommand() - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner
This builds, runs the command and outputs it to the logger as it is being run

S

saveBuilder(String) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Save this builder as a JSON file in order to be able to reuse it in place
setArguments(List<String>) - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner
This is the code you actually want to run after 'python'.
setEnvironmentNameOrPath(String) - Method in class qupath.ext.biop.cellpose.CellposeSetup
 
setEnvironmentType(VirtualEnvironmentRunner.EnvType) - Method in class qupath.ext.biop.cellpose.CellposeSetup
 
setVersion(CellposeSetup.CellposeVersion) - Method in class qupath.ext.biop.cellpose.CellposeSetup
 

T

tileHeight - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
tileSize(int) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Size in pixels of a tile used for detection.
tileSize(int, int) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Size in pixels of a tile used for detection.
tileWidth - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
toString() - Method in enum qupath.ext.biop.cellpose.CellposeSetup.CellposeVersion
 
toString() - Method in enum qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
 
train() - Method in class qupath.ext.biop.cellpose.Cellpose2D
 
trainDirectory - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 

U

useGPU - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
useGPU() - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Use a GPU for prediction or training.
useOmnipose - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
useOmnipose() - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Use Omnipose implementation: Adds --omni flag to command

V

valDirectory - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
valueOf(String) - Static method in enum qupath.ext.biop.cellpose.CellposeSetup.CellposeVersion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
Returns the enum constant of this type with the specified name.
values() - Static method in enum qupath.ext.biop.cellpose.CellposeSetup.CellposeVersion
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
Returns an array containing the constants of this enum type, in the order they are declared.
VENV - qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
 
VirtualEnvironmentRunner - Class in qupath.ext.biop.cmd
A wrapper to run python virtualenvs, that tries to figure out the commands to run based on the environment type
VirtualEnvironmentRunner(String, VirtualEnvironmentRunner.EnvType) - Constructor for class qupath.ext.biop.cmd.VirtualEnvironmentRunner
 
VirtualEnvironmentRunner.EnvType - Enum in qupath.ext.biop.cmd
This enum helps us figure out the type of virtualenv.
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