helperFunctions/createScanimageMetadataStruct.m at master · HarveyLab/helperFunctions · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
function siStruct = createScanimageMetadataStruct

% Create scanimage metadata structure:
siStruct = struct();

% Fields relevant for Acquisition2P that you have to change depending on
% your movie file:
siStruct.SI4.scanFramePeriod = 0.0380596; % Inverse of frame rate: (frames per second)^-1

% Fields relevant for Acquisition2P that most likely should NOT be changed:
siStruct.SI4.fastZEnable = false; % Whether fast Z scanning (3D volume acquisition) is switched on);
siStruct.SI4.channelsSave = 1; % Which channels are saved (1=green/GCaMP, 2=red);
siStruct.SI4.stackNumSlices = 1; % How many slices are acquired during volume scanning (leave at 1).
siStruct.SI4.fastZDiscardFlybackFrames = 1; % How many frames are discarded during flyback during volume scanning.

% Other fields saved by scanimage (not currently used by Acquisition2P, but
% included here for completeness):
siStruct.SI4.acqFrameBufferLength = 2;
siStruct.SI4.acqFrameBufferLengthMin = 2;
siStruct.SI4.acqFramesDone = 0;
siStruct.SI4.acqNumAveragedFrames = 1;
siStruct.SI4.acqNumFrames = 100000;
siStruct.SI4.acqState = 'idle';
siStruct.SI4.beamDirectMode = false;
siStruct.SI4.beamFillFracAdjust = 0;
siStruct.SI4.beamFlybackBlanking = 1;
siStruct.SI4.beamLengthConstants = Inf;
siStruct.SI4.beamLiveAdjust = true;
siStruct.SI4.beamPowerLimits = 100;
siStruct.SI4.beamPowerUnits = 'percent';
siStruct.SI4.beamPowers = 100;
siStruct.SI4.beamPzAdjust = false;
siStruct.SI4.cfgFilename = 'C:\data\config\scanimage\matthias.cfg';
siStruct.SI4.channelsAutoReadOffsets = false;
siStruct.SI4.channelsAutoReadOffsetsOnFocus = false;
siStruct.SI4.channelsDataType = 'int16';
siStruct.SI4.channelsDisplay = 1;
siStruct.SI4.channelsInputRange = {[0 0.2] [0 0.2] [0 4] [0 4]};
siStruct.SI4.channelsLUT = [-100 8191;0 5556;0 8191;0 8191];
siStruct.SI4.channelsMergeColor = {'green' 'red' 'gray' 'none'};
siStruct.SI4.channelsMergeEnable = false;
siStruct.SI4.channelsMergeFocusOnly = false;
siStruct.SI4.channelsOffset = [-275;-483;22;33];
siStruct.SI4.channelsSubtractOffset = [true;true;false;false];
siStruct.SI4.displayFrameBatchFactor = 1;
siStruct.SI4.displayFrameBatchFactorLock = false;
siStruct.SI4.displayFrameBatchSelectLast = 0;
siStruct.SI4.displayFrameBatchSelection = 1;
siStruct.SI4.displayRollingAverageFactor = 1;
siStruct.SI4.displayRollingAverageFactorLock = 0;
siStruct.SI4.displayShowCrosshair = false;
siStruct.SI4.errorCondition = false;
siStruct.SI4.errorConditionIdentifiers = {};
siStruct.SI4.errorConditionMessages = {};
siStruct.SI4.fastCfgAutoStartTf = [false;false;false;false;false;false];
siStruct.SI4.fastCfgAutoStartType = {[];[];[];[];[];[]};
siStruct.SI4.fastCfgCfgFilenames = {'';'';'';'';'';''};
siStruct.SI4.fastZAcquisitionDelay = 0.015;
siStruct.SI4.fastZActive = false;
siStruct.SI4.fastZAllowLiveBeamAdjust = false;
siStruct.SI4.fastZDiscardFlybackFrames = 1;
siStruct.SI4.fastZFillFraction = [];
siStruct.SI4.fastZFramePeriodAdjustment = -100;
siStruct.SI4.fastZImageType = 'XY-Z';
siStruct.SI4.fastZNumDiscardFrames = 1;
siStruct.SI4.fastZNumVolumes = 2000;
siStruct.SI4.fastZPeriod = [];
siStruct.SI4.fastZScanType = 'sawtooth';
siStruct.SI4.fastZSettlingTime = 0.03;
siStruct.SI4.fastZUseAOControl = true;
siStruct.SI4.fastZVolumesDone = 0;
siStruct.SI4.focusDuration = 120;
siStruct.SI4.frameAcqFcnDecimationFactor = 1;
siStruct.SI4.loggingEnable = 1;
siStruct.SI4.loggingFileCounter = 1;
siStruct.SI4.loggingFileCounterAutoReset = true;
siStruct.SI4.loggingFilePath = 'D:\data\Matthias\MM052\MM052_141217';
siStruct.SI4.loggingFileStem = 'MM052_141217_task';
siStruct.SI4.loggingFramesPerFile = 1000;
siStruct.SI4.loggingFramesPerFileLock = false;
siStruct.SI4.loggingMaxFileSize = [];
siStruct.SI4.loopNumRepeats = Inf;
siStruct.SI4.loopRepeatPeriod = 10;
siStruct.SI4.loopRepeatsDone = 0;
siStruct.SI4.maxFrameEventRate = 65;
siStruct.SI4.motorFastMotionThreshold = 100;
siStruct.SI4.motorHasMotor = true;
siStruct.SI4.motorHasSecondMotor = false;
siStruct.SI4.motorMoveTimeout = 5;
siStruct.SI4.motorSecondMotorZEnable = false;
siStruct.SI4.motorUserDefinedPositions = {};
siStruct.SI4.pmtEnable = [];
siStruct.SI4.pmtGain = [];
siStruct.SI4.scanAngleMultiplierFast = 1;
siStruct.SI4.scanAngleMultiplierSlow = 1;
siStruct.SI4.scanFOVAngularRangeFast = 13.2;
siStruct.SI4.scanFOVAngularRangeSlow = 13.2;
siStruct.SI4.scanFillFraction = 0.66;
siStruct.SI4.scanFillFractionSpatial = 0.860742;
siStruct.SI4.scanForceSquarePixel = true;
siStruct.SI4.scanForceSquarePixelation = true;
siStruct.SI4.scanFramePeriod = 0.0380596;
siStruct.SI4.scanFrameRate = 26.2746;
siStruct.SI4.scanFramesStarted = 0;
siStruct.SI4.scanLinePeriod = 6.32111e-05;
siStruct.SI4.scanLinesPerFrame = 512;
siStruct.SI4.scanMinZoomFactor = 1;
siStruct.SI4.scanMode = 'bidirectional';
siStruct.SI4.scanParamCache = [];
siStruct.SI4.scanPhase = 49;
siStruct.SI4.scanPhaseFine = 0;
siStruct.SI4.scanPhaseFineMap = NaN;
siStruct.SI4.scanPhaseMap = NaN;
siStruct.SI4.scanPixelTimeMaxMinRatio = 1.96836;
siStruct.SI4.scanPixelTimeMean = 9.4708e-08;
siStruct.SI4.scanPixelsPerLine = 512;
siStruct.SI4.scanZoomFactor = 1;
siStruct.SI4.secondsCounter = 4.86;
siStruct.SI4.shutterDelay = 0;
siStruct.SI4.stackEndPower = NaN;
siStruct.SI4.stackNumSlices = 1;
siStruct.SI4.stackReturnHome = true;
siStruct.SI4.stackSlicesDone = 0;
siStruct.SI4.stackStartCentered = 0;
siStruct.SI4.stackStartPower = NaN;
siStruct.SI4.stackUseStartPower = false;
siStruct.SI4.stackUserOverrideLz = false;
siStruct.SI4.stackZEndPos = NaN;
siStruct.SI4.stackZStartPos = NaN;
siStruct.SI4.stackZStepSize = -5;
siStruct.SI4.statusString = 'Acquisition idle';
siStruct.SI4.triggerExtStartTrigPreScan = true;
siStruct.SI4.triggerExtStartTrigTimeout = 30;
siStruct.SI4.triggerExtTrigEnable = false;
siStruct.SI4.triggerMaxLoopInterval = 42.95;
siStruct.SI4.triggerMaxLoopIntervalFrames = 10000;
siStruct.SI4.triggerNextTrigEdge = 'rising';
siStruct.SI4.triggerNextTrigMode = 'advance';
siStruct.SI4.triggerNextTrigSrc = [];
siStruct.SI4.triggerStartTrigEdge = 'rising';
siStruct.SI4.triggerStartTrigSrc = [];
siStruct.SI4.triggerTimestampResolution = 1e-08;
siStruct.SI4.userFunctionsCfg = NaN;
siStruct.SI4.userFunctionsOverride = NaN;
siStruct.SI4.userFunctionsUsr = NaN;
siStruct.SI4.usrPropListCurrent = {'triggerExtStartTrigTimeout';'focusDuration';'acqFrameBufferLengthMin';'fastCfgCfgFilenames';'fastCfgAutoStartTf';'fastCfgAutoStartType';'beamPzAdjust';'beamDirectMode';'beamLengthConstants';'stackUserOverrideLz';'userFunctionsUsr';'displayShowCrosshair';'channelsLUT';'channelsMergeColor';'channelsMergeEnable';'channelsMergeFocusOnly';'channelsAutoReadOffsetsOnFocus';'channelsSubtractOffset';'scanParamCache';'pmtGain';'pmtEnable';'loggingFileCounterAutoReset'};
siStruct.SI4.triggerClockTimeFirst = '17-12-2014 11:13:19.248';
siStruct.SI4.triggerFrameNumber = 1;
siStruct.SI4.triggerFrameStartTime = 0;
siStruct.SI4.triggerTime = -0.38697616;