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‎Igor Procedures/HDF5 - Shortcut.lnk‎

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‎Igor Procedures/Load_SBScripts.ipf‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,10 @@
1+
#pragma TextEncoding = "UTF-8"
2+
#pragma rtGlobals=3 // Use modern global access method and strict wave access
3+
#pragma DefaultTab={3,20,4} // Set default tab width in Igor Pro 9 and later
4+
5+
#include "ROI_overlay"
6+
#include "Correct4DImport"
7+
#include "custom_export"
8+
#include "RoiShift"
9+
#include "split_group3d"
10+
#include "loaders"

‎Igor Procedures/OS_GUI - Shortcut.lnk‎

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‎Igor Procedures/OS_GUI.ipf.lnk‎

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‎Igor Procedures/wxw - Shortcut.lnk‎

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‎User Procedures/OS/NoiseArray3D.ibw‎

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‎User Procedures/OS/NoiseArray4LEDs.ibw‎

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‎User Procedures/OS/OS_AutoROIs_SD.ipf‎

Lines changed: 3 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -24,14 +24,13 @@ variable Display_RoiMask = OS_Parameters[%Display_Stuff]
2424
variable SD_minimum = OS_Parameters[%ROI_SD_min]
2525
variable ROI_minsize = OS_Parameters[%ROI_minPx]
2626
variable ROI_maxsize = OS_Parameters[%ROI_maxPx]
27-
variable ROI_minpx = OS_Parameters[%ROI_minpix]
27+
variable ROI_minpx = OS_Parameters[%ROI_minPx]
2828
variable GaussSize = OS_Parameters[%ROI_GaussSize]
2929
variable adjacentPix = OS_Parameters[%ROIGap_px]
3030
variable X_cut = OS_Parameters[%LightArtifact_cut]
3131
variable LineDuration = OS_Parameters[%LineDuration]
3232
variable nLifesLeft = 10
3333
variable nPxBinning = OS_Parameters[%ROI_PxBinning]
34-
variable FOV_at_zoom065 = OS_Parameters[%FOV_at_zoom065] * (OS_Parameters[%fullFOVSize]/0.5)
3534

3635
variable nROIs_max = 1000
3736

@@ -44,12 +43,8 @@ variable nY = Dimsize(wDataCh0_detrended,1)
4443
variable nLayers = Dimsize(wDataCh0_detrended,2)
4544
variable GaussFilter = 1
4645

47-
wave wParamsNum // Reads data-header
48-
variable zoom = wParamsNum(30) // extract zoom
49-
variable px_Size = (0.65/zoom * FOV_at_zoom065)/nX // microns
50-
variable MaxPixelRoi = ROI_maxsize//floor((pi * (ROI_maxsize^2))/(px_Size^2))
51-
variable MinPixelRoi = ROI_minsize//floor((pi * (ROI_minsize^2))/(px_Size^2))
52-
46+
variable MaxPixelRoi = ROI_maxsize
47+
variable MinPixelRoi = ROI_minsize
5348

5449
duplicate /o wDataCh0_detrended wDataCh0_mask
5550

@@ -156,7 +151,6 @@ nY = DimSize(wDataCh0_detrended,1)
156151
if (MinPixelRoi<ROI_minpx) // exception handling - don't allow ROIs smaller than ROI_minpx pixels
157152
MinPixelRoi=ROI_minpx
158153
endif
159-
print "Pixel Size:", round(px_size*100)/100," microns"
160154
print MinPixelRoi, "-", MaxPixelRoi, "pixels per ROI"
161155
string input_name = "wDataCh"+Num2Str(Channel)+"_detrended"
162156
duplicate /o $input_name InputData
@@ -423,10 +417,6 @@ endfor
423417
duplicate /o ROIs_order ROIs
424418
killwaves ROI_id, ROIs_order
425419

426-
// setscale
427-
setscale /p x,-nX/2*px_Size,px_Size,"µm" Stack_SD, ROIs
428-
setscale /p y,-nY/2*px_Size,px_Size,"µm" Stack_SD, ROIs
429-
430420
variable rr
431421
if (Display_RoiMask==1)
432422
display /k=1

‎User Procedures/OS/OS_AutoRoiByCorr.ipf‎

Lines changed: 4 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -41,14 +41,11 @@ variable useMask4Corr = OS_Parameters[%useMask4Corr]
4141
variable X_cut = OS_Parameters[%LightArtifact_cut]
4242
variable LineDuration = OS_Parameters[%LineDuration]
4343
variable nPxBinning = OS_Parameters[%ROI_PxBinning]
44-
variable FOV_at_zoom065 = OS_Parameters[%FOV_at_zoom065] * (OS_Parameters[%fullFOVSize]/0.5)
45-
4644

4745
variable nLifesLeft = 10
4846
variable nROIs_absolute_Max = 1000 // does not allow going over 1000 here, otherwise start to get memory issues
4947

5048
// data handling
51-
wave wParamsNum // Reads data-header
5249
string input_name = "wDataCh"+Num2Str(Channel)+"_detrended"
5350
duplicate /o $input_name InputData
5451
variable nX = DimSize(InputData,0)
@@ -78,14 +75,6 @@ else
7875
endif
7976
variable nRois_max = (nX-X_cut/nPxBinning)*nY
8077

81-
82-
// calculate Pixel / ROI sizes in microns
83-
variable zoom = wParamsNum(30) // extract zoom
84-
variable px_Size = (0.65/zoom * FOV_at_zoom065)/nX // microns
85-
variable px_Size_Full = (0.65/zoom * FOV_at_zoom065)/nX_Full // microns
86-
87-
88-
print "Pixel Size:", round(px_Size_Full*100)/100," microns"
8978
print ROI_minpx, "-", ROI_maxpx, "pixels per ROI"
9079
variable nPx_neighbours = 1
9180

@@ -326,8 +315,6 @@ if (useMask4Corr==1)
326315
// fix CellLab Scaling
327316
wave wROI=root:CellLab2D:Stack_ave:waves:wROI
328317
wave wDisplay=root:CellLab2D:Stack_ave:waves:wDisplay
329-
setscale /p x,-nX/2*px_Size_Full,px_Size_Full,"µm" wROI, wDisplay
330-
setscale /p y,-nY/2*px_Size_Full,px_Size_Full,"µm" wROI, wDisplay
331318
//
332319
wave ROIs
333320
duplicate /o ROIs ROIs_input
@@ -352,10 +339,6 @@ if (useMask4Corr==1)
352339
endif
353340
endif
354341

355-
// setscale
356-
357-
setscale /p x,-nX_Full/2*px_Size_Full,px_Size_Full,"µm" Stack_Ave, ROIs, Correlation_projection
358-
setscale /p y,-nY_Full/2*px_Size_Full,px_Size_Full,"µm" Stack_Ave, ROIs, Correlation_projection
359342

360343
// display
361344
if (Display_RoiMask==1)
@@ -382,9 +365,12 @@ if (Display_RoiMask==1)
382365
endfor
383366
endif
384367

368+
// kill infs/NaN
369+
Correlation_projection[][]=(NumType(Correlation_projection[p][q])==0)?(Correlation_projection[p][q]):(0)
370+
385371

386372
// cleanup
387373
killwaves InputData,W_Statslinearcorrelationtest,currentwave_main,currentwave_comp, correlation_projection_sub, allRois
388-
killwaves currentRoi,M_colors,InputDataBinDiv,ROIs_new
374+
killwaves currentRoi,InputDataBinDiv,ROIs_new
389375

390376
end

‎User Procedures/OS/OS_AveragingSuite.ipf‎

Lines changed: 6 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -101,24 +101,6 @@ for (pp=0;pp<nPlanes;pp+=1)
101101
killwaves TempStack2
102102
endfor
103103

104-
//variable nY_per_plane = nY / nPlanes
105-
//make /o/n=(nX * nSubStacks,nY_per_plane,nF_SubStacks * nPlanes) AverageStack0_Chopped_byPlane = NaN
106-
//make /o/n=(nX ,nY_per_plane,nF_SubStacks * nPlanes * nSubStacks) AverageStack0_DoubleChopped = NaN
107-
//for (pp=0;pp<nPlanes;pp+=1)
108-
// variable Currentplane = pp + (AverageStack_FirstPlane -1)
109-
// if (CurrentPlane > (nPlanes-1))
110-
// CurrentPlane-=nPlanes
111-
// endif
112-
// make /o/n=(nX * nSubStacks,nY_per_plane,nF_SubStacks) TempStack = AverageStack0_Chopped[p][q+CurrentPlane*nY_per_Plane][r]
113-
// AverageStack0_Chopped_byPlane[][][pp*nF_SubStacks,(pp+1)*nF_SubStacks-1]=TempStack[p][q][r-pp*nF_SubStacks]
114-
// for (ss=0;ss<nSubStacks;ss+=1)
115-
// SubStart = TriggerTimes_Frame[ss*AverageStack_Chopup] - TriggerTimes_Frame[0]
116-
// make /o/n=(nX,nY_per_plane,nF_SubStacks) TempStack2 = TempStack[p+ss*nX][q][r]
117-
// AverageStack0_DoubleChopped[][][pp*nF_SubStacks*nSubStacks+ss*nF_SubStacks,pp*nF_SubStacks*nSubStacks+(ss+1)*nF_SubStacks-1]=TempStack2[p][q][r-(pp*nF_SubStacks*nSubStacks+ss*nF_SubStacks)]
118-
// endfor
119-
// killwaves TempStack2
120-
//endfor
121-
122104
if (AverageStack_SavePlanes==1)
123105
imagesave /s/f/t="tiff" AverageStack0_Chopped_byPlane
124106
endif
@@ -166,11 +148,11 @@ if (waveexists($"Triggertimes")==0)
166148
DoUpdate
167149
endif
168150
// 5 // check if Averages"N" is there
169-
if (waveexists($"Averages"+Num2Str(Channel))==0)
170-
print "Warning: Averages wave not yet generated - doing that now..."
171-
OS_BasicAveraging()
172-
DoUpdate
173-
endif
151+
//if (waveexists($"Averages"+Num2Str(Channel))==0)
152+
//print "Warning: Averages wave not yet generated - doing that now..."
153+
//OS_BasicAveraging() - makes it loop if AverageStack0 not jet made...
154+
//DoUpdate
155+
//endif
174156
// 6 // check if AverageStack0" is there
175157
if (waveexists($"AverageStack"+Num2Str(Channel))==0)
176158
print "Warning: AverageStack0 wave not yet generated - please compute that first..."
@@ -192,7 +174,7 @@ variable/G gContrastLow = 55500
192174
variable/G gContrastHigh = 57000
193175
variable/G gContrastGain = 3
194176

195-
variable/G gEndlessLoop = 1
177+
variable/G gEndlessLoop = 0
196178
variable/G gLoopStimuli = 1
197179

198180

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