Index

A

activateFindThreshold() (napari_bigfish.bigfishapp.BigfishApp method) activateRemoveDuplicates() (napari_bigfish.bigfishapp.BigfishApp method) addBatchButton() (napari_bigfish.DetectFISHSpotsWidget method) addBatchParameterWidget() (napari_bigfish.DetectFISHSpotsBatchWidget method) addCountSpotsWidget() (napari_bigfish.DetectFISHSpotsWidget method) addDecomposeDenseRegionsWidget() (napari_bigfish.DetectFISHSpotsWidget method)

addDetectSpotsWidget() (napari_bigfish.DetectFISHSpotsWidget method) addInputImagesWidget() (napari_bigfish.DetectFISHSpotsBatchWidget method) addRunButton() (napari_bigfish.DetectFISHSpotsBatchWidget method) addSpotCountingTable() (napari_bigfish.DetectFISHSpotsWidget method) addSubtractBackgroundWidget() (napari_bigfish.DetectFISHSpotsWidget method) alphaSignal (napari_bigfish.bigfishapp.BigfishApp attribute) ArrayUtil (class in napari_bigfish.array_util)

B

betaSignal (napari_bigfish.bigfishapp.BigfishApp attribute)

BigfishApp (class in napari_bigfish.bigfishapp)

C

copyDataToClipboard() (napari_bigfish.qtutil.TableView method)

countSpotsPerCellAndEnvironment() (napari_bigfish.bigfishapp.BigfishApp method) createEmptySpotCountReport() (napari_bigfish.bigfishapp.BigfishApp method)

D

deactivateFindThreshold() (napari_bigfish.bigfishapp.BigfishApp method) deactivateRemoveDuplicates() (napari_bigfish.bigfishapp.BigfishApp method) decomposeDenseRegions() (napari_bigfish.bigfishapp.BigfishApp method)

decomposeRadiusSignal (napari_bigfish.bigfishapp.BigfishApp attribute) DetectFISHSpotsBatchWidget (class in napari_bigfish) DetectFISHSpotsWidget (class in napari_bigfish) detectSpots() (napari_bigfish.bigfishapp.BigfishApp method)

F

findThresholdChanged() (napari_bigfish.DetectFISHSpotsWidget method)

findThresholdSignal (napari_bigfish.bigfishapp.BigfishApp attribute)

G

gammaSignal (napari_bigfish.bigfishapp.BigfishApp attribute) getAlpha() (napari_bigfish.bigfishapp.BigfishApp method) getBeta() (napari_bigfish.bigfishapp.BigfishApp method) getComboInput() (napari_bigfish.qtutil.WidgetTool static method) getData() (napari_bigfish.bigfishapp.BigfishApp method) getDataOfLayerWithName() (napari_bigfish.napari_util.NapariUtil method) getDecomposeRadiusXY() (napari_bigfish.bigfishapp.BigfishApp method) getDecomposeRadiusZ() (napari_bigfish.bigfishapp.BigfishApp method) getDecomposeSpotRadius() (napari_bigfish.bigfishapp.BigfishApp method) getGamma() (napari_bigfish.bigfishapp.BigfishApp method) getLabelLayers() (napari_bigfish.napari_util.NapariUtil method) getLayersOfType() (napari_bigfish.napari_util.NapariUtil method)

getLineInput() (napari_bigfish.qtutil.WidgetTool static method) getPointsLayers() (napari_bigfish.napari_util.NapariUtil method) getRadiusXY() (napari_bigfish.bigfishapp.BigfishApp method) getRadiusZ() (napari_bigfish.bigfishapp.BigfishApp method) getResult() (napari_bigfish.bigfishapp.BigfishApp method) getScale() (napari_bigfish.bigfishapp.BigfishApp method) getSelectedDataAsString() (napari_bigfish.qtutil.TableView method) getSigmaXY() (napari_bigfish.bigfishapp.BigfishApp method) getSigmaZ() (napari_bigfish.bigfishapp.BigfishApp method) getSpotCountPerCellAndEnvironment() (napari_bigfish.bigfishapp.BigfishApp method) getSpotRadius() (napari_bigfish.bigfishapp.BigfishApp method) getSpots() (napari_bigfish.bigfishapp.BigfishApp method) getThreshold() (napari_bigfish.bigfishapp.BigfishApp method)

K

keyPressEvent() (napari_bigfish.qtutil.TableView method)

M

make_sample_data() (in module napari_bigfish) module napari_bigfish napari_bigfish.array_util napari_bigfish.bigfishapp napari_bigfish.napari_util napari_bigfish.qtutil

N

napari_bigfish module napari_bigfish.array_util module napari_bigfish.bigfishapp module

napari_bigfish.napari_util module napari_bigfish.qtutil module NapariUtil (class in napari_bigfish.napari_util)

O

onClickBatch() (napari_bigfish.DetectFISHSpotsWidget method) onClickCountSpots() (napari_bigfish.DetectFISHSpotsWidget method) onClickDecomposeDenseRegions() (napari_bigfish.DetectFISHSpotsWidget method) onClickDetectSpots() (napari_bigfish.DetectFISHSpotsWidget method) onClickSubtractBackground() (napari_bigfish.DetectFISHSpotsWidget method)

onDecomposeChanged() (napari_bigfish.DetectFISHSpotsBatchWidget method) onFindThresholdChanged() (napari_bigfish.DetectFISHSpotsWidget method) onLayerAddedOrRemoved() (napari_bigfish.DetectFISHSpotsWidget method) onLayerLoaded() (napari_bigfish.DetectFISHSpotsBatchWidget method) onRemoveDuplicatesChanged() (napari_bigfish.DetectFISHSpotsWidget method) onSubtractBackgroundChanged() (napari_bigfish.DetectFISHSpotsBatchWidget method)

P

progressSignal (napari_bigfish.bigfishapp.BigfishApp attribute)

R

radiusChanged() (napari_bigfish.DetectFISHSpotsWidget method) radiusSignal (napari_bigfish.bigfishapp.BigfishApp attribute) removeDuplicatesChanged() (napari_bigfish.DetectFISHSpotsWidget method) removeDuplicatesSignal (napari_bigfish.bigfishapp.BigfishApp attribute)

replaceItemsInComboBox() (napari_bigfish.qtutil.WidgetTool static method) reportSpotCounts() (napari_bigfish.bigfishapp.BigfishApp method) reportSpots() (napari_bigfish.bigfishapp.BigfishApp method) runBatch() (napari_bigfish.bigfishapp.BigfishApp method) (napari_bigfish.DetectFISHSpotsBatchWidget method)

S

setAlpha() (napari_bigfish.bigfishapp.BigfishApp method) setBeta() (napari_bigfish.bigfishapp.BigfishApp method) setData() (napari_bigfish.bigfishapp.BigfishApp method) setDecomposeRadiusXY() (napari_bigfish.bigfishapp.BigfishApp method) setDecomposeRadiusZ() (napari_bigfish.bigfishapp.BigfishApp method) setGamma() (napari_bigfish.bigfishapp.BigfishApp method) setModel() (napari_bigfish.DetectFISHSpotsBatchWidget method) (napari_bigfish.DetectFISHSpotsWidget method) setProgress() (napari_bigfish.bigfishapp.BigfishApp method) setProgressMax() (napari_bigfish.bigfishapp.BigfishApp method)

setRadiusXY() (napari_bigfish.bigfishapp.BigfishApp method) setRadiusZ() (napari_bigfish.bigfishapp.BigfishApp method) setSigmaXY() (napari_bigfish.bigfishapp.BigfishApp method) setSigmaZ() (napari_bigfish.bigfishapp.BigfishApp method) setThreshold() (napari_bigfish.bigfishapp.BigfishApp method) shallFindThreshold() (napari_bigfish.bigfishapp.BigfishApp method) shallRemoveDuplicates() (napari_bigfish.bigfishapp.BigfishApp method) sigmaChanged() (napari_bigfish.DetectFISHSpotsWidget method) sigmaSignal (napari_bigfish.bigfishapp.BigfishApp attribute) stripZeroRowsAndColumns() (napari_bigfish.array_util.ArrayUtil static method) subtractBackground() (napari_bigfish.bigfishapp.BigfishApp method)

T

TableView (class in napari_bigfish.qtutil)

thresholdChanged() (napari_bigfish.DetectFISHSpotsWidget method) thresholdSignal (napari_bigfish.bigfishapp.BigfishApp attribute)

U

updateAlpha() (napari_bigfish.DetectFISHSpotsWidget method) updateBeta() (napari_bigfish.DetectFISHSpotsWidget method) updateDecomposeRadiusXY() (napari_bigfish.DetectFISHSpotsWidget method) updateDecomposeRadiusZ() (napari_bigfish.DetectFISHSpotsWidget method) updateGamma() (napari_bigfish.DetectFISHSpotsWidget method) updateLayerSelectionComboBoxes() (napari_bigfish.DetectFISHSpotsWidget method)

updateRadiusXY() (napari_bigfish.DetectFISHSpotsWidget method) updateRadiusZ() (napari_bigfish.DetectFISHSpotsWidget method) updateScaleXY() (napari_bigfish.DetectFISHSpotsBatchWidget method) updateScaleZ() (napari_bigfish.DetectFISHSpotsBatchWidget method) updateSigmaXY() (napari_bigfish.DetectFISHSpotsWidget method) updateSigmaZ() (napari_bigfish.DetectFISHSpotsWidget method) updateThreshold() (napari_bigfish.DetectFISHSpotsWidget method)

W

WidgetTool (class in napari_bigfish.qtutil)