Index
All Classes and Interfaces|All Packages
A
- addParameter(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Generic means of adding a spotiflow parameter
- addParameter(String, String) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Generic means of adding a spotiflow parameter
B
- build() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Create a
Spotiflow, all ready for detection. - builder() - Static method in class qupath.ext.biop.spotiflow.Spotiflow
-
Create a builder to customize detection parameters.
C
- channels - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- channels(int...) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Specify channels.
- channels(String...) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Specify channels by name.
- classChannelName - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- closeWatchService() - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner
- CONDA - Enum constant in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
D
- detectObjects(ImageData<BufferedImage>, String, Collection<? extends PathObject>) - Method in class qupath.ext.biop.spotiflow.Spotiflow
-
Detect cells within one or more parent objects, firing update events upon completion.
- doSubpixel - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- doSubpixel(boolean) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Allows to go subpixel resolution
E
- EXE - Enum constant in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
G
- getChangedFiles() - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner
- getCondaPath() - Method in class qupath.ext.biop.spotiflow.SpotiflowSetup
- getDescription() - Method in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
- getDescription() - Method in class qupath.ext.biop.spotiflow.SpotiflowExtension
- getInstance() - Static method in class qupath.ext.biop.spotiflow.SpotiflowSetup
- getName() - Method in class qupath.ext.biop.spotiflow.SpotiflowExtension
- getProcess() - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner
- getProcessLog() - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner
- getQuPathVersion() - Method in class qupath.ext.biop.spotiflow.SpotiflowExtension
- getRepository() - Method in class qupath.ext.biop.spotiflow.SpotiflowExtension
- getSpotiflowPythonPath() - Method in class qupath.ext.biop.spotiflow.SpotiflowSetup
H
- helpPredict() - Method in class qupath.ext.biop.spotiflow.Spotiflow
-
Prints the help and the available CLI arguments for the prediction command
- helpTrain() - Method in class qupath.ext.biop.spotiflow.Spotiflow
-
Prints the help and the available CLI arguments for the training command
I
- installExtension(QuPathGUI) - Method in class qupath.ext.biop.spotiflow.SpotiflowExtension
M
- minDistance - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- modelDir - Variable in class qupath.ext.biop.spotiflow.Spotiflow
O
- OTHER - Enum constant in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
P
- parameters - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- pathClass - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- pretrainedModelName - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- probabilityThreshold - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- process3d - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- process3d(boolean) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Allows to process all slices
Q
- qupath.ext.biop.cmd - package qupath.ext.biop.cmd
- qupath.ext.biop.spotiflow - package qupath.ext.biop.spotiflow
R
- runCommand(boolean) - 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
- savePredictionImages - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- savePredictionImages(boolean) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Set input folder to predict spots
- setArguments(List<String>) - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner
-
This is the code you actually want to run after 'python'.
- setClass(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Allows to go subpixel resolution
- setClassChannelName() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Allows to go subpixel resolution
- setCondaPath(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowSetup
- setMinDistance(double) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Set minimum distance between spots for NMS
- setModelDir(File) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Set model directory to use for prediction
- setPretrainedModelName(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Set pre-trained model to use for prediction
- setProbabilityThreshold(double) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Set probability threshold for peak detection
- setSpotiflowPythonPath(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowSetup
- setTrainingInputDir(File) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Set input folder to train a new model
- setTrainingOutputDir(File) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Set output folder to save a new model
- Spotiflow - Class in qupath.ext.biop.spotiflow
-
Spot detection based on the following method:
- Spotiflow() - Constructor for class qupath.ext.biop.spotiflow.Spotiflow
- SpotiflowBuilder - Class in qupath.ext.biop.spotiflow
-
Spot detection based on the following method:
- SpotiflowBuilder() - Constructor for class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Build a spotiflow model
- SpotiflowExtension - Class in qupath.ext.biop.spotiflow
-
Install Spotiflow as an extension.
- SpotiflowExtension() - Constructor for class qupath.ext.biop.spotiflow.SpotiflowExtension
- spotiflowSetup - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- SpotiflowSetup - Class in qupath.ext.biop.spotiflow
- SpotiflowSetup() - Constructor for class qupath.ext.biop.spotiflow.SpotiflowSetup
- startWatchService(Path) - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner
T
- tempDirectory - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- tempDirectory(File) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Set input folder to predict spots
- toString() - Method in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
- trainingInputDir - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- trainingOutputDir - Variable in class qupath.ext.biop.spotiflow.Spotiflow
U
- useGPU - Variable in class qupath.ext.biop.spotiflow.Spotiflow
- useGPU(boolean) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder
-
Enable CPU / GPU usage
V
- valueOf(String) - Static method in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
-
Returns the enum constant of this class with the specified name.
- values() - Static method in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- VENV - Enum constant in enum class 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(String, VirtualEnvironmentRunner.EnvType, String, String) - Constructor for class qupath.ext.biop.cmd.VirtualEnvironmentRunner
- VirtualEnvironmentRunner.EnvType - Enum Class in qupath.ext.biop.cmd
-
This enum helps us figure out the type of virtualenv.
All Classes and Interfaces|All Packages