B C D E F G I L M N O P Q R S T U V
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All Classes All Packages
All Classes All Packages
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
- 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
- getQuPathVersion() - Method in class qupath.ext.biop.cellpose.CellposeExtension
- getRepository() - Method in class qupath.ext.biop.cellpose.CellposeExtension
- 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
- 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
- showTrainingGraph() - Method in class qupath.ext.biop.cellpose.Cellpose2D
-
Displays a JavaFX graph as a dialog so you can inspect the Losses per epoch
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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