├── .gitignore ├── ChangeLog.txt ├── ExampleCodeSnippets ├── AcquisitionAutoResume │ ├── abortOnFrame.m │ └── readme.md ├── PI_Build_Example_C863.m ├── Prior_Basic.m ├── Zaber_Build_Example.m ├── example_connect_Soloist.m └── readme.txt ├── ExampleConfigFiles ├── SIBT_settings.yml ├── ScanImage │ ├── Machine_Data_File_LinScan_SIMULATED.m │ └── README.txt ├── componentSettings.m ├── frameSizes.yml └── systemSettings.yml ├── LICENSE ├── Release_Announcements ├── Release_20th_June_2021.txt ├── Release_21st_September_2021.txt ├── Release_22nd_September_2022.txt └── Release_7th_December_2021.txt ├── SETTINGS ├── .gitignore └── laser_calibration │ └── .gitignore ├── SETTINGS_BACKUP └── .gitignore ├── addBTtopath.m ├── code ├── +BakingTray │ ├── +acq │ │ └── estimateFinishedTime.m │ ├── +channelChooser │ │ ├── four_channels_settings.yml │ │ ├── loadEmissionSpectrum.m │ │ ├── loadExcitationSpectrum.m │ │ ├── readSettings.m │ │ └── settings.yml │ ├── +gui │ │ ├── @acquisition_view │ │ │ ├── acquisition_view.m │ │ │ ├── areaSelector.m │ │ │ ├── bake_callback.m │ │ │ ├── buildFigure.m │ │ │ ├── getThresholdAndOverlayGrid.m │ │ │ ├── imageZoomHandler.m │ │ │ ├── overlayBoundingBoxesOnImage.m │ │ │ ├── overlayLastBoundingBoxes.m │ │ │ ├── overlayPointsOnImage.m │ │ │ ├── overlaySlideFrostedAreaOnImage.m │ │ │ ├── overlayStageBoundariesOnImage.m │ │ │ ├── overlayStagePositionOnImage.m │ │ │ ├── overlayThreshBorderOnImage.m │ │ │ ├── overlayTileGridOnImage.m │ │ │ ├── pause_callback.m │ │ │ ├── removeOverlays.m │ │ │ ├── setChannelToView.m │ │ │ ├── setDepthToView.m │ │ │ ├── setupListeners.m │ │ │ ├── spawnTilePickerWindow.m │ │ │ ├── startPreviewScan.m │ │ │ ├── stop_callback.m │ │ │ ├── updateBakeButtonState.m │ │ │ ├── updateSectionImage.m │ │ │ └── zoomOutToShowSlide.m │ │ ├── @laser_view │ │ │ └── laser_view.m │ │ ├── @prepare_view │ │ │ ├── autoTrim.m │ │ │ ├── buildWindow.m │ │ │ ├── executeJogMotion.m │ │ │ ├── icons │ │ │ │ ├── left_double_arrow.tiff │ │ │ │ └── left_single_arrow.tiff │ │ │ ├── isSafeToMove.m │ │ │ ├── positionNextToBakingTrayView.m │ │ │ ├── prepare_view.m │ │ │ ├── private │ │ │ │ └── hMover_KeyPress.m │ │ │ ├── resetBladeIfNeeded.m │ │ │ ├── stopAllAxes.m │ │ │ ├── takeNslices.m │ │ │ ├── takeOneSlice.m │ │ │ └── toggleEnable.m │ │ ├── @view │ │ │ ├── buildWindow.m │ │ │ ├── displayMessage.m │ │ │ ├── enableDisableThisView.m │ │ │ ├── importFrameSizeSettings.m │ │ │ ├── loadRecipe.m │ │ │ ├── newSample.m │ │ │ ├── populateRecipePanel.m │ │ │ ├── startChannelChooserGUI.m │ │ │ ├── startLaserGUI.m │ │ │ ├── startPrepareGUI.m │ │ │ ├── startPreviewSampleGUI.m │ │ │ ├── updateAllRecipeEditBoxesAndStatusText.m │ │ │ ├── updateRecipePropertyInRecipeClass.m │ │ │ ├── updateStatusText.m │ │ │ ├── updateTileSizeLabelText.m │ │ │ └── view.m │ │ ├── child_view.m │ │ ├── newGenericGUIFigureWindow.m │ │ ├── newGenericGUIPanel.m │ │ └── questdlgchckbox.m │ ├── +settings │ │ ├── devNotes.txt │ │ ├── dummy.m │ │ ├── installLocation.m │ │ ├── parseComPort.m │ │ ├── private │ │ │ ├── Do_Not_Edit │ │ │ ├── componentSettings_empty.m │ │ │ ├── defaultRecipe.m │ │ │ ├── default_BT_Settings.m │ │ │ └── readme.txt │ │ ├── readComponentSettings.m │ │ ├── readDefaultRecipe.m │ │ ├── readRecipe.m │ │ ├── readSystemSettings.m │ │ └── settingsLocation.m │ ├── +slack │ │ ├── MakeSlackAttachment.m │ │ ├── README.md │ │ ├── SendSlackNotification.m │ │ ├── notify.m │ │ └── private │ │ │ ├── README_JSONLAB.txt │ │ │ ├── http_createHeader.m │ │ │ ├── http_paramsToString.m │ │ │ ├── jsonopt.m │ │ │ ├── loadjson.m │ │ │ ├── loadubjson.m │ │ │ ├── mergestruct.m │ │ │ ├── savejson.m │ │ │ ├── saveubjson.m │ │ │ ├── urlread2.m │ │ │ ├── urlread_notes.txt │ │ │ └── varargin2struct.m │ ├── +utils │ │ ├── addLaserCalib.m │ │ ├── centerFigureInScreen.m │ │ ├── clearSerial.m │ │ ├── doesPathContainAnAcquisition.m │ │ ├── fitSigmoidToData.m │ │ ├── generateSupportReport.m │ │ ├── getGitInfo.m │ │ ├── listLaserCalib.m │ │ ├── measureSurfaceHeight.m │ │ ├── messageWindow.m │ │ ├── readAcqLogFile.m │ │ ├── readSectionLogFile.m │ │ ├── returnDiskSpace.m │ │ ├── turbo.m │ │ └── wavelength2rgb.m │ ├── +yaml │ │ ├── DateTime.m │ │ ├── MIT-license.txt │ │ ├── README.md │ │ ├── ReadYaml.m │ │ ├── ReadYamlRaw.m │ │ ├── Tests │ │ │ ├── Data │ │ │ │ ├── test_import │ │ │ │ │ ├── file1.yaml │ │ │ │ │ ├── file2.yaml │ │ │ │ │ ├── file3.yaml │ │ │ │ │ ├── file4.yaml │ │ │ │ │ ├── import.mat │ │ │ │ │ ├── import.yaml │ │ │ │ │ ├── import_def.mat │ │ │ │ │ ├── import_def.yaml │ │ │ │ │ └── import_nonex.yaml │ │ │ │ ├── test_inheritance │ │ │ │ │ ├── inheritance.mat │ │ │ │ │ ├── inheritance.yaml │ │ │ │ │ ├── inheritance_loop.yaml │ │ │ │ │ ├── inheritance_multiple.mat │ │ │ │ │ └── inheritance_multiple.yaml │ │ │ │ ├── test_misc │ │ │ │ │ ├── bug6.yaml │ │ │ │ │ ├── dos_CRLF.yaml │ │ │ │ │ ├── miscellaneous.yaml │ │ │ │ │ ├── spec_chars_utf8.yaml │ │ │ │ │ └── unix_LF.yaml │ │ │ │ └── test_primitives │ │ │ │ │ ├── floating_points.mat │ │ │ │ │ ├── floating_points.yaml │ │ │ │ │ ├── indentation.mat │ │ │ │ │ ├── indentation.yaml │ │ │ │ │ ├── matrices.mat │ │ │ │ │ ├── matrices.yaml │ │ │ │ │ ├── sequence_mapping.mat │ │ │ │ │ ├── sequence_mapping.yaml │ │ │ │ │ ├── simple.mat │ │ │ │ │ ├── simple.yaml │ │ │ │ │ ├── time.mat │ │ │ │ │ ├── time.yaml │ │ │ │ │ ├── time_variants.mat │ │ │ │ │ ├── time_variants.yaml │ │ │ │ │ ├── usecase_struct_01.mat │ │ │ │ │ ├── usecase_struct_01.yaml │ │ │ │ │ └── whitespaces.yaml │ │ │ ├── selftest_report.html │ │ │ ├── selftest_yamlmatlab.m │ │ │ ├── test_ReadYaml.m │ │ │ └── test_WriteYaml.m │ │ ├── WriteYaml.m │ │ ├── datadump.m │ │ ├── deflateimports.m │ │ ├── doinheritance.m │ │ ├── dosubstitution.m │ │ ├── external │ │ │ ├── LICENSE-2.0.txt │ │ │ └── snakeyaml-1.9.jar │ │ ├── extras │ │ │ ├── GetYamlVals.m │ │ │ └── TimeVals2Cell.m │ │ ├── iscolumnvector.m │ │ ├── ismymatrix.m │ │ ├── isord.m │ │ ├── isrowvector.m │ │ ├── issingle.m │ │ ├── kwd_parent.m │ │ ├── makematrices.m │ │ ├── merge_struct.m │ │ └── mergeimports.m │ ├── @channelChooser │ │ ├── buildFigure.m │ │ ├── channelChooser.m │ │ ├── determineChansToSave.m │ │ ├── determineLaserWavelength.m │ │ ├── emission_spectra │ │ │ ├── alexa647.txt │ │ │ ├── dii.txt │ │ │ ├── dio.txt │ │ │ ├── ebfp.txt │ │ │ ├── ecfp.txt │ │ │ ├── egfp.txt │ │ │ ├── eyfp.txt │ │ │ ├── mcherry.txt │ │ │ └── tdtomato.txt │ │ ├── excitation_spectra_2p │ │ │ ├── README.txt │ │ │ ├── alexa647.txt │ │ │ ├── citrine_w.txt │ │ │ ├── dii.txt │ │ │ ├── dio.txt │ │ │ ├── ebfp.txt │ │ │ ├── ecfp.txt │ │ │ ├── egfp.txt │ │ │ ├── eyfp.txt │ │ │ ├── mcherry.txt │ │ │ └── tdtomato.txt │ │ ├── plotChanBand.m │ │ ├── plotEmissionSpectrum.m │ │ └── plotExcitationSpectrum.m │ └── getObject.m ├── @BT │ ├── BT.m │ ├── abortSlicing.m │ ├── applyLaserCalibrationToScanner.m │ ├── attachCutter.m │ ├── attachLaser.m │ ├── attachMotionAxes.m │ ├── attachRecipe.m │ ├── attachScanner.m │ ├── bake.m │ ├── checkAttachedStages.m │ ├── checkIfAcquisitionIsPossible.m │ ├── checkIfCuttingIsPossible.m │ ├── convertImageCoordsToStagePosition.m │ ├── convertStagePositionToImageCoords.m │ ├── defineSavePath.m │ ├── displayMessage.m │ ├── estimateTimeRemaining.m │ ├── genAutoTrimSequence.m │ ├── getNextROIs.m │ ├── getThreshold.m │ ├── initialisePreviewImageData.m │ ├── logPositionToPositionArray.m │ ├── placeNewTilesInPreviewData.m │ ├── populateCurrentTilePattern.m │ ├── preAllocateTileBuffer.m │ ├── private │ │ ├── bakeCleanupFun.m │ │ └── resume_GUI_helper.m │ ├── renewLaserConnection.m │ ├── reportAcquisitionSize.m │ ├── resumeAcquisition.m │ ├── returnPreviewStructure.m │ ├── runTileScan.m │ ├── slack.m │ ├── sliceSample.m │ ├── takeRapidPreview.m │ └── tilesRemaining.m ├── BTresources │ ├── LimitFigSize.m │ ├── NumTiles.m │ ├── TileStepSize.m │ ├── affineMatGen.m │ ├── assessAverage.m │ ├── plotboxpos.m │ ├── prettyTime.m │ ├── previewFilesToStack.m │ ├── wizard.m │ └── wizardpage.m ├── BakingTray.m ├── autoROI │ ├── +autoROI │ │ ├── +autothresh │ │ │ ├── batchDir.m │ │ │ ├── plot.m │ │ │ └── run.m │ │ ├── +batchtest │ │ │ ├── evaluatePerformance.m │ │ │ ├── readme.txt │ │ │ └── runEvaluation.m │ │ ├── +evaluate │ │ │ ├── areTestStructuresEqual.m │ │ │ ├── compareResults.m │ │ │ ├── genComparisonTable.m │ │ │ ├── genSummaryTable.m │ │ │ ├── getSummaryTable.m │ │ │ ├── plotResults.m │ │ │ ├── printFileNamesAsDoubleColumnTable.m │ │ │ ├── private │ │ │ │ └── plotSettings.m │ │ │ └── report_auto_thresh_notes.m │ │ ├── +groundTruth │ │ │ ├── genBordersForAllInDir.m │ │ │ ├── genGroundTruthBorders.m │ │ │ ├── previewMatFilesToImStack.m │ │ │ ├── removeSmallestBorder.m │ │ │ ├── replaceRecipe.m │ │ │ └── stackToGroundTruth.m │ │ ├── +plotting │ │ │ ├── bt_auto_compare.m │ │ │ ├── overlayTileGrid.m │ │ │ ├── showBoundingBoxesForSection.m │ │ │ └── viewStackResult.m │ │ ├── +test │ │ │ ├── evaluateROIs.m │ │ │ ├── getAllFirstImages.m │ │ │ ├── printNonPStack.m │ │ │ ├── private │ │ │ │ └── handle_runDir.m │ │ │ ├── runOnAllInDir.m │ │ │ └── runOnStackStruct.m │ │ ├── +tools │ │ │ ├── fixMicsPix.m │ │ │ ├── getGitInfo.m │ │ │ ├── reportRecipeName.m │ │ │ ├── resizeAllInDir.m │ │ │ └── resizePStack.m │ │ ├── binarizeImage.m │ │ ├── boundingBoxToTiledBox.m │ │ ├── findTissueAtROIedges.m │ │ ├── genOverlapStack.m │ │ ├── getBoundingBoxes.m │ │ ├── getForegroundBackgroundPixels.m │ │ ├── getSubImageUsingBoundingBox.m │ │ ├── mergeOverlapping.m │ │ ├── obtainCleanBackgroundSD.m │ │ ├── overlayBoundingBox.m │ │ ├── overlayBoundingBoxes.m │ │ ├── readSettings.m │ │ ├── removeCornerEdgeArtifacts.m │ │ ├── rescaleAndFilterImage.m │ │ ├── shiftROIsBasedOnStageFrontLeft.m │ │ └── validateBoundingBox.m │ ├── .gitignore │ └── autoROI.m └── components │ ├── @recipe │ ├── autoSetCutSize.m │ ├── checkIfAcquisitionIsPossible.m │ ├── devNotes.txt │ ├── estimatedSizeOnDisk.m │ ├── recipe.m │ ├── recipe2struct.m │ ├── recordScannerSettings.m │ ├── saveRecipe.m │ ├── setCurrentPositionAsCuttingPosition.m │ ├── setCurrentPositionAsFrontLeft.m │ ├── setFrontLeftFromVentralMidLine.m │ ├── tilePattern.m │ └── writeFullRecipeForAcquisition.m │ ├── cutting │ ├── FaulhaberMCDC.m │ ├── JaneliaLeicaController.m │ ├── SWCserialCutter.m │ ├── buildCutterComponent.m │ ├── cutter.m │ └── dummyCutter.m │ ├── laser │ ├── buildLaserComponent.m │ ├── chameleon.m │ ├── dummyLaser.m │ ├── laser.m │ ├── maitai.m │ └── tiberius.m │ ├── logger │ ├── bkFileLogger.m │ └── loghandler.m │ ├── motion │ ├── AMS_SIN11.m │ ├── AVS_100_25.m │ ├── BSC201_APT.m │ ├── BSC201_Troubleshooting.txt │ ├── C663.m │ ├── C863.m │ ├── C891.m │ ├── DRV014.m │ ├── analog_controller.m │ ├── buildMotionComponent.m │ ├── dummy_linearcontroller.m │ ├── dummy_linearstage.m │ ├── ensemble.m │ ├── genericPIcontroller.m │ ├── genericPIstage.m │ ├── genericPriorstage.m │ ├── genericStage.m │ ├── genericZaberController.m │ ├── generic_AeroTechZJack.m │ ├── haydon43K4U.m │ ├── linearcontroller.m │ ├── linearstage.m │ ├── singleAxisPriorController.m │ └── soloist.m │ └── scanning │ ├── +SIBT │ ├── closeAllHistogramWindows.m │ ├── get_hSICtl_from_base.m │ └── get_hSI_from_base.m │ ├── @SIBT │ ├── SIBT.m │ ├── applyLaserCalibration.m │ ├── applyScanSettings.m │ ├── applyZstackSettingsFromRecipe.m │ ├── armScanner.m │ ├── doScanSettingsMatchRecipe.m │ ├── moveFastZTo.m │ ├── private │ │ ├── default_SIBT_settings.m │ │ ├── default_frameSizes.yml │ │ └── readSIBTsettings.m │ ├── returnScanSettings.m │ ├── setImageSize.m │ └── tileAcqDone.m │ ├── @dummyScanner │ ├── acquireTile.m │ ├── attachPreviewStack.m │ ├── createFigureWindow.m │ ├── dummyScanner.m │ ├── initiateTileScan.m │ ├── private │ │ └── writeSignedTiff.m │ ├── readFrameSizeSettings.m │ └── returnDefaultScanSettings.m │ ├── buildScannerComponent.m │ ├── devNotes.txt │ └── scanner.m ├── diagnostic ├── BT_timer.m ├── lookForDuplicateTilesInCache.m ├── measureTilingAccuracy.m ├── measuring_xy_accuracy │ ├── +mxy │ │ ├── @camera │ │ │ ├── .gitignore │ 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