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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 previously 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
 
CELLPOSE_1 - qupath.ext.biop.cellpose.CellposeSetup.CellposeVersion
 
CELLPOSE_2 - 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.
EXE - qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
 

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
 
getOutputLog() - Method in class qupath.ext.biop.cellpose.Cellpose2D
Returns the log from running the cellpose command, with any error messages and status updates of the cellpose process You can use this during training or prediction
getQCResults() - Method in class qupath.ext.biop.cellpose.Cellpose2D
Get the results table associated with the Quality Control run
getQuPathVersion() - Method in class qupath.ext.biop.cellpose.CellposeExtension
 
getRepository() - Method in class qupath.ext.biop.cellpose.CellposeExtension
 
getTrainingDirectory() - Method in class qupath.ext.biop.cellpose.Cellpose2D
The directory that was used for saving the training images
getTrainingResults() - Method in class qupath.ext.biop.cellpose.Cellpose2D
Returns a parsed version of the cellpose log as a ResultsTable with columns Epoch, Time, Loss, Loss Test and LR
getValidationDirectory() - Method in class qupath.ext.biop.cellpose.Cellpose2D
The directory that was used for saving the validation images
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.
minTrainMasks - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 
minTrainMasks(Integer) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
 
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
 
OMNIPOSE_034 - 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
saveTrainingImages() - Method in class qupath.ext.biop.cellpose.Cellpose2D
Save training images for the project
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
 
setOverlap(int) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
Set the overlap (in pixels) between tiles.
setVersion(CellposeSetup.CellposeVersion) - Method in class qupath.ext.biop.cellpose.CellposeSetup
 
showTrainingGraph() - Method in class qupath.ext.biop.cellpose.Cellpose2D
Overloaded method for backwards compatibility.
showTrainingGraph(boolean, boolean) - Method in class qupath.ext.biop.cellpose.Cellpose2D
Displays a JavaFX graph as a dialog, so you can inspect the Losses per epoch also saves the graph to the QC folder if requested
simplify(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder
 
simplifyDistance - Variable in class qupath.ext.biop.cellpose.Cellpose2D
 

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
Executes the cellpose training by 1.
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, String) - 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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