napari_bigfish package

Submodules

• napari_bigfish.array_util module
  • ArrayUtil
    • ArrayUtil.stripZeroRowsAndColumns()
• napari_bigfish.bigfishapp module
  • BigfishApp
    • BigfishApp.activateFindThreshold()
    • BigfishApp.activateRemoveDuplicates()
    • BigfishApp.alphaSignal
    • BigfishApp.betaSignal
    • BigfishApp.countSpotsPerCellAndEnvironment()
    • BigfishApp.createEmptySpotCountReport()
    • BigfishApp.deactivateFindThreshold()
    • BigfishApp.deactivateRemoveDuplicates()
    • BigfishApp.decomposeDenseRegions()
    • BigfishApp.decomposeRadiusSignal
    • BigfishApp.detectSpots()
    • BigfishApp.findThresholdSignal
    • BigfishApp.gammaSignal
    • BigfishApp.getAlpha()
    • BigfishApp.getBeta()
    • BigfishApp.getData()
    • BigfishApp.getDecomposeRadiusXY()
    • BigfishApp.getDecomposeRadiusZ()
    • BigfishApp.getDecomposeSpotRadius()
    • BigfishApp.getGamma()
    • BigfishApp.getRadiusXY()
    • BigfishApp.getRadiusZ()
    • BigfishApp.getResult()
    • BigfishApp.getScale()
    • BigfishApp.getSigmaXY()
    • BigfishApp.getSigmaZ()
    • BigfishApp.getSpotCountPerCellAndEnvironment()
    • BigfishApp.getSpotRadius()
    • BigfishApp.getSpots()
    • BigfishApp.getThreshold()
    • BigfishApp.progressSignal
    • BigfishApp.radiusSignal
    • BigfishApp.removeDuplicatesSignal
    • BigfishApp.reportSpotCounts()
    • BigfishApp.reportSpots()
    • BigfishApp.runBatch()
    • BigfishApp.setAlpha()
    • BigfishApp.setBeta()
    • BigfishApp.setData()
    • BigfishApp.setDecomposeRadiusXY()
    • BigfishApp.setDecomposeRadiusZ()
    • BigfishApp.setGamma()
    • BigfishApp.setProgress()
    • BigfishApp.setProgressMax()
    • BigfishApp.setRadiusXY()
    • BigfishApp.setRadiusZ()
    • BigfishApp.setSigmaXY()
    • BigfishApp.setSigmaZ()
    • BigfishApp.setThreshold()
    • BigfishApp.shallFindThreshold()
    • BigfishApp.shallRemoveDuplicates()
    • BigfishApp.sigmaSignal
    • BigfishApp.subtractBackground()
    • BigfishApp.thresholdSignal
• napari_bigfish.napari_util module
  • NapariUtil
    • NapariUtil.getDataOfLayerWithName()
    • NapariUtil.getLabelLayers()
    • NapariUtil.getLayersOfType()
    • NapariUtil.getPointsLayers()
• napari_bigfish.qtutil module
  • TableView
    • TableView.copyDataToClipboard()
    • TableView.getSelectedDataAsString()
    • TableView.keyPressEvent()
  • WidgetTool
    • WidgetTool.getComboInput()
    • WidgetTool.getLineInput()
    • WidgetTool.replaceItemsInComboBox()

Module contents

class napari_bigfish.DetectFISHSpotsBatchWidget(napari_viewer, model)

Bases: QWidget

The widget that lets the user select images and start the batch-processing. The widget has input fields for the scale in xy and z, checkboxes for the options subtract background and decompose dense regions, image-lists for the input images, the cell labels and the nuclei masks and an action button to start the batch-processing.

addBatchParameterWidget()

addInputImagesWidget()

addRunButton()

onDecomposeChanged(state)

onLayerLoaded(event)

onSubtractBackgroundChanged(state)

runBatch()

setModel(aModel)

updateScaleXY(text)

updateScaleZ(text)

class napari_bigfish.DetectFISHSpotsWidget(napari_viewer)

Bases: QWidget

The widget allows to parametrize and run background subtraction and spot detection on the active image.

The widget regroups the operations subtract background, detect spots, decompose dense regions and count spots. It also has a button to change to the Batch Processing-widget, which will use the parameters entered here.

addBatchButton()

Adds an action button that closes this widget and opens the batch- processing widget. The model, containg the parameters are transferred to the new widget.

addCountSpotsWidget()

Add the widget for the Spot Counting operation to the layout. The widget has combo-boxes for the selection of the points-layer containing the spots, the labels layer containing the cells and the labels-layer containing the nuclei. It has an action button to run the operation.

addDecomposeDenseRegionsWidget()

Add the widget for the Dense Region Decomposition to the layout. The widget has a combo-box for the selection of the points-layer containing the previously detected spots. It has input fields for the spot radius and for the alpha, beta and gamma parameters. It has an action button to run the operation on the active image layer.

addDetectSpotsWidget()

Adds the widget for the spot detection to the layout. The widget has an input field for the threshold, input fields for the spot radius, checkboxes for the remove duplicates``and ``find threshold options and an action button to run the operation.

addSpotCountingTable(table)

addSubtractBackgroundWidget()

Adds the widget for the background subtration to the layout. The widget has two input fields for the sigma of the Gaussian in xy and z and an action button to run the operation.

findThresholdChanged(state)

onClickBatch()

onClickCountSpots()

onClickDecomposeDenseRegions()

onClickDetectSpots()

onClickSubtractBackground()

onFindThresholdChanged(state)

onLayerAddedOrRemoved(event: Event)

onRemoveDuplicatesChanged(state)

radiusChanged(radiusXY, radiusZ)

removeDuplicatesChanged(state)

setModel(aModel)

sigmaChanged(sigmaXY, sigmaZ)

thresholdChanged(threshold)

updateAlpha(text)

updateBeta(text)

updateDecomposeRadiusXY(text)

updateDecomposeRadiusZ(text)

updateGamma(text)

updateLayerSelectionComboBoxes()

updateRadiusXY(text)

updateRadiusZ(text)

updateSigmaXY(text)

updateSigmaZ(text)

updateThreshold(text)

napari_bigfish.make_sample_data()

Download and return a sample image for the napari-bigfish plugin. The dataset has three layers, one image layer with the FISH-spots, one artificially constructed labels-layer, representing cells and one also artificially constructed labels layer, representing the nuclei.