pro PNs_gcamp common data common vars common CFD common CFDconst ;tiff: 0,45,2,10,17,21,2,1,7 ;on raw data: 0,45,2,10,15,240,2,1,7,5 does not work yet ;coordinates: 0,45,2,9,17,21,4,1,7,4 ;New TIFFs : 1,45,2,10,21,33,4,1,7,4,0 ;New coordinates: 1,45,2,9,21,21,4,1,7,4 ;export glomeruli time courses: 0,45,2,11,15,x,4,0,7,0,x,x ;IN COMMON VARS colortable = 39;0;43;41 ;45 for TIFF output, 0 for black/white; 37 for blue_black_red_white; 38 for black_red_white ;set flags here ;loading the data and calculate signals flag[view_loadExp] = 3;3;4 ; 0 for old setup, to 1 for Visicam, 2 for confocal flag[view_CalcMethod] = 3500; 3550: bleachcorrect,excludstim ;3150: bleachcorrect,excludstim,withinAl ;3750: bleachcorrect, excludestim, addnoise ;4950; 3 (original data); 10 for fura ; for bleaching is incluiding in 9 and 10 ;***** normalerweise 7 oder 8, schnelle Berechnung 0 flag[csm_median] = 0; !!!!!!!!!!!!!!!change!!!!!!! 0: no correction, 1: median in space fixed values, 2: space and time fixed values; 3: space and time, using flag values flag(csm_median_space)= 3 flag(csm_median_time) = 0 flag[csm_movement] = 0; movement correction; 3: to include the movcorr from mathias´ program flag[CSM_DataShift] = 1 ; shift data instead of mask flag[le_shrinkFaktor] = 1 ;no shrinkfaktor with 1 flag[RM_separateLayers] = 0 ;separates the layers in exportGlomeruli and SingleOverviews ;view the data analysis flag[view_reportMethod] =1003;1003: for mathias´program; 11;10;-1 ; check in subloop.pro ; 10: TIFF-Ausgabe, 11: Traces-Berechnung, 12 : Movie; 13 : stack of tiff files; 19:CTV + Glodatamix; 14: .RAW; 15: single tiff files firstframe = 1 ;for movie output lastframe = 4 ;spacefilter: ft_radius wird nur benutzt, wenn FilterSpaceFlag gesetzt ist ;der zusätzliche SpaceFilter wird nur ausgeführt, wenn er gt 2 ist. flag[ft_radius] =3 ; setting 5 gives ca 25microns squares with 20x Obj in traces calculation FilterSpaceFlag = 0 ;***** normalerweise 1, schnelle Berechnung 0 FilterSpaceSize = 0;***** normalerweise 2, schnelle Berechnung 0 FilterTimeFlag = 0 FilterTimeSize = 0 flag[so_indiScale] = 0;7;1500;1101; 3 ; ShowOverviews : 0:scale according to values in control window ; 1 = scale each overviewframe to its own min/max ; 2 = scale to min/max of all ; 3 to central region of individual frame ; 5 to selected area of individual frame ; 2x scales both neg and positive with the same dynamics ; setting also affects scaling in the movie output, see exprotmovie.pro ; 7 in export movie: bottom fixed, top in area region scalemax = 3.000 scalemin = -1.0 flag[rm_fotoOK] =0;1;1;5 ; draw coordinate positions in TIFF output as white squares flag[so_method] = 0 ; ShowOverviews Method: 1: mittleres Signal wŠhren Stimulus ;0 for selecting CTV_method in the file CurveToValue.pro in ShowOverviews folder ;10 for selecting CTV_method in the file Overview10ctv.pro in ShowOverviews folder ;11 for correlation flag[RM_differentViews] = 0 ;mirrors right ALs following the name in the list flag[LE_UseFirstBuffer] = 1;0; flag[so_morphoBackgr] = 0;150;150 flag[so_morphoBackgrNeg]= 0;95;105 flag[so_withinMask] =0 flag[CTV_scalebar] = 0 flag[LE_StartBackground] = 4; frame where background calculation starts (in general startbackground:stim_on frames are used for background calculation) flag[LE_PrestimEndBackground] = 0 ;How many frames before stimulus to stop with background. Default: 2 flag[RM_ROITrace] =0 flag[VIEW_ScatterLightFactor] = 1;for the 3xxx and 4xxx family with scattered light correction, this factor gives the strength of the unsharp mask. Default: 1 ; no change flags CorrectFlag = 0;1;0 ;0:unkorrigiert, 1:luftkorrigiert flag[macSystem] = 0 flag[view_initCorr] = -1;3;-1;1050;21;21;17 ; initial correction when loading data, -1 (= 15) for no correction at all (save memory) flag[batchMode] = 1 flag[le_AskForAir] = 0;1;0 flag[trueColour] = 1 flag[rm_plotTrace] = 0;1 ; reportMask, plots traces to screen when set flag[rm_printAscii] = 0 ; ReportMask, flag[rm_PrintLine] = 1 ; ReportMask flag[view_MultiExp] = 0 ; 0 for single experiment flag[pta_plottimerange] = 0 ; PlotTraceArray if set, takes range from control window flag[pta_plotMeanValue] = 0 ; PlotTraceArray ;pfade für Clementina auswertungMother = 'K:\PNs\' DatenMother = 'K:\PNs\data\' ;path settings for all measurements ;location of the coordinate files flag[stg_OdorMaskPath] = auswertungMother+ 'IDLcoors\' ;woher kommt die Maske ? ;path for the .lst files flag[stg_OdorInfoPath] = auswertungMother+ 'IDLlisten\' ;ReportPath, place for the IDL output ;flag[stg_OdorReportPath] = auswertungMother+ 'IDLoutput\' ;wohin soll die Ausgabe ? und pharma (ttx, ptx, etc) flag[stg_OdorReportPath] = auswertungMother+ '\IDLoutput\' ;for concentration exps ;flag[stg_OdorReportPath] = 'H:\ana\analysis_LNs\IDLoutput\'; in external hard disk ;flag[stg_OdorReportPath] = auswertungMother+ 'synII\IDLoutput\' ;for concentration exps longMeasurements = 1 shortMeasurements = 0 ;one block for each animal follows, with specic settings IF longMeasurements THEN begin flag[CTV_method] = -222;-12;-379;50;21;100;21 ;22: take 3 frames aroung lastframe - 3 frames around firstframe firstframe = 7 ;for movie output lastframe = 13 average_flag = 0 ; set to 0 for single measurements, 1 for averages, 2 for both PNs_measu_gcamp, DatenMother ;, average_flag endIF ;longMeasurements IF shortMeasurements THEN begin flag[view_CalcMethod] = 12554; 5 (original data); 10 for fura ; for bleaching is incluiding in 9 and 10 ;***** normalerweise 7 oder 8, schnelle Berechnung 0 firstframe = 1 ;for movie output lastframe = 4 flag[CTV_method] = 22;50;21;100;21 ;22: take 3 frames aroung lastframe - 3 frames around firstframe ;flag[CTV_method] = 300;50;21;100;21 ;22: take 3 frames aroung lastframe - 3 frames around firstframe ;colortable = 0 ;CorrectFlag = 1 endIF ;shortMeasurements end