Package qupath.ext.biop.spotiflow

Class SpotiflowBuilder

java.lang.Object
qupath.ext.biop.spotiflow.SpotiflowBuilder
public class SpotiflowBuilder extends Object
Spot detection based on the following method: 
   Albert Dominguez Mantes et al.
     "Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression"
   Cold Spring Harbor Laboratory - bioRxiv, 2024. doi: 10.1101/2024.02.01.578426
See the main repo at https://github.com/weigertlab/spotiflow

Very much inspired by qupath-extension-cellpose at https://github.com/BIOP/qupath-extension-cellpose

  • Constructor Details

    • SpotiflowBuilder

      protected SpotiflowBuilder()
      Build a spotiflow model

  • Method Details

    • tempDirectory

      public SpotiflowBuilder tempDirectory(File inputDir)
      Set input folder to predict spots
      Parameters:
      inputDir - path to prediction input dir
      Returns:
      this builder

    • savePredictionImages

      @Deprecated public SpotiflowBuilder savePredictionImages(boolean savePredictionImages)
      Deprecated.
      use cleanTempDir() instead
      Set input folder to predict spots
      Parameters:
      savePredictionImages - overwrite variable
      Returns:
      this builder

    • cleanTempDir

      public SpotiflowBuilder cleanTempDir()
      clear all files in the tem
      Returns:
      this builder

    • setPretrainedModelName

      public SpotiflowBuilder setPretrainedModelName(String modelName)
      Set pre-trained model to use for prediction
      Parameters:
      modelName - name of the pre-trained model
      Returns:
      this builder

    • setProbabilityThreshold

      public SpotiflowBuilder setProbabilityThreshold(double probabilityThreshold)
      Set probability threshold for peak detection
      Parameters:
      probabilityThreshold -
      Returns:
      this builder

    • setMinDistance

      public SpotiflowBuilder setMinDistance(double minDistance)
      Set minimum distance between spots for NMS
      Parameters:
      minDistance -
      Returns:
      this builder

    • setModelDir

      public SpotiflowBuilder setModelDir(File modelDir)
      Set model directory to use for prediction
      Parameters:
      modelDir - path to the custom model
      Returns:
      this builder

    • channels

      public SpotiflowBuilder channels(int... channels)
      Specify channels. Useful for detecting nuclei for one channel within a multi-channel image, or potentially for trained models that support multi-channel input.
      Parameters:
      channels - 0-based indices of the channels to use
      Returns:
      this builder

    • channels

      public SpotiflowBuilder channels(String... channels)
      Specify channels by name. Useful for detecting nuclei for one channel within a multichannel image, or potentially for trained models that support multichannel input.
      Parameters:
      channels - channels names to use
      Returns:
      this builder

    • setTrainingInputDir

      public SpotiflowBuilder setTrainingInputDir(File inputDir)
      Set input folder to train a new model
      Parameters:
      inputDir - path to the training input dir
      Returns:
      this builder

    • setTrainingOutputDir

      public SpotiflowBuilder setTrainingOutputDir(File outputDir)
      Set output folder to save a new model
      Parameters:
      outputDir - path to the training input dir
      Returns:
      this builder

    • disableGPU

      public SpotiflowBuilder disableGPU()
      Forces using CPU instead of GPU
      Returns:
      this builder

    • process3d

      @Deprecated public SpotiflowBuilder process3d(boolean process3d)
      Deprecated.
      use process3d() instead
      Allows to process all slices
      Parameters:
      process3d - override process3d
      Returns:
      this builder

    • process3d

      public SpotiflowBuilder process3d()
      Allows to process all slices of 3D stack. Has to be used together with a 3D-model (custom or pre-trained)
      Returns:
      this builder

    • doSubpixel

      public SpotiflowBuilder doSubpixel(boolean doSubpixel)
      Allows to go subpixel resolution
      Parameters:
      doSubpixel - override doSubpixel
      Returns:
      this builder

    • setClassChannelName

      public SpotiflowBuilder setClassChannelName()
      Allows to go subpixel resolution
      Returns:
      this builder

    • nThreads

      public SpotiflowBuilder nThreads(int nThreads)
      Specify the number of threads to use for processing. If you encounter problems, setting this to 1 may help to resolve them by preventing multithreading.
      Parameters:
      nThreads - the number of threads to use
      Returns:
      this builder

    • setClass

      public SpotiflowBuilder setClass(String pathClass)
      Allows to go subpixel resolution
      Returns:
      this builder

    • saveBuilder

      public SpotiflowBuilder saveBuilder(String name)
      Save this builder as a JSON file in order to be able to reuse it in place
      Parameters:
      name - A name to append to the JSON file. Keep it meaningful for your needs
      Returns:
      this builder

    • saveTempImagesAsOmeZarr

      public SpotiflowBuilder saveTempImagesAsOmeZarr()
      True to save images in the temp folder as OME-Zarr files. Otherwise, saved as OME-TIFF WARNING : OME-Zarr option is only available from spotiflow >= 0.5.8
      Returns:
      this builder

    • clearAllChildObjects

      public SpotiflowBuilder clearAllChildObjects()
      Remove all child objects (i.e. previous points) from the parent shapes
      Returns:
      this builder

    • clearChildObjectsBelongingToCurrentChannels

      public SpotiflowBuilder clearChildObjectsBelongingToCurrentChannels()
      Remove child objects (i.e. previous points) from the parent shapes which belongs to the current selected channel(s) i.e. which have the same class as the channel name. Should be used together with setClassChannelName() to have the desired effect.
      Returns:
      this builder

    • addParameter

      public SpotiflowBuilder addParameter(String flagName, String flagValue)
      Generic means of adding a spotiflow parameter
      Parameters:
      flagName - the name of the flag, e.g. "save_every"
      flagValue - the value that is linked to the flag, e.g. "20". Can be an empty string or null if it is not needed
      Returns:
      this builder

    • addParameter

      public SpotiflowBuilder addParameter(String flagName)
      Generic means of adding a spotiflow parameter
      Parameters:
      flagName - the name of the flag, e.g. "save_every"
      Returns:
      this builder

    • build

      public Spotiflow build()
      Create a Spotiflow, all ready for detection.
      Returns:
      a new Spotiflow instance