// Astrocyte Calcium Imaging Toolbox 
// by Wilson Adams, Vanderbilt Biophotonics Center

// Last Updated: 18 Sept 2018

// Import Image Sequence
// GFB LUT
macro "Green Fire Blue LUT Action Tool - C000F123dC0bfF723dF423dC0f0F723dCff0Fa23dCfffFd23d" {
    run("Green Fire Blue");
    if (getWidth==256 && getHeight==32)
        rename("Green Fire Blue");
}
// B/C 
macro "Adjust Brightness and Contrast Action Tool - C333DabDbaCaaaD5cDcaDd7Dd8C888D3dD4dD4eD5eD6cD6eDc9De4De5De6De7De8De9CdddD4bDb4C555D88D97Da6Db6CdddD24D2bD42Db2C999D5dDadDdaCfffD25D37D38D45D46D47D48D49D52D55D56D57D58D64D65D66D67D68D74D75D76D77D84D85D86D94D95Da2Da4C555D5bD6aD79D7aD89D8cD98Da7Da8Db7CcccD14D15D16D17D18D19D1aD1bD23D32D41D51D61D71D81D91Da1Db1Dc2C888Dc6DccDd3Dd4CeeeD2aD4aD59C777D7eD8eD9cD9eDaeDbdDbeDcdDdbDdcDeaDebCaaaD4cD6dD7dD8dDacDbbDc4Dd6Dd9C444D6bD7bD7cD8aD99Da9Db8Dc7Dc8CcccD2cDc3CeeeD33C666Db5C999D9dDbcDcbDd5C444D8bD9aD9bDaaDb9CbbbD3cD5aD69D78D87D96Da5CbbbDc5" {
    run("Brightness/Contrast...");
}
// Flatfield Correction Tool
macro "Automated Flatfield Correction Action Tool - C037T0b11FT6b09FTcb09C" {
	
}
// Z-project Tool (Default max)
macro "Maximum Intensity Projection Action Tool (+space = Mean; +shift = StDev; +alt = Sum)  - C6abD44D62C577D05D23D24D41D42De1CfffD18D19D98D99Db6Db7Dd4Dd5C033D1eD2eD3eD4eD5eD6eD7eD8eD9eDbcDdaC8bbDa5Dc3C795D6cCfffD15D16D17D25D33D35D43D45D51D53D55D61D63D65D71D73D75D81D83D85D91D93D95D96D97Da1Da3Db1Db3Db4Db5Dc1Dd1Dd2Dd3Df0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDffC000DbeDdcC5aeD26D36C798Da9Dc7C255D0cDe8CeffD1bD9bDb9Dd7C9a7D2cC6abD84Da2C588D01D02D03D04D11D12D13D14D20D21D22D30D31D32D40D50D60D70D80D90Da0Db0Dc0Dd0De0C144DadDcbCcedD68C7a9Da7Dc5C122D00C6bdD39C366D09De5CeffD1aD1dD9aD9dDb8DbbDd6Dd9Cbb9D2bC6abD54D64D72D74D82D92CaddD87C798Da8Dc6C022D0eDaeDccDeaC6beD57D66D76C366D0aD10De6Cac8D7aC5adD27C244D0dDacDcaDe9CeffD1cD2dD3dD4dD5dD6dD7dD8dD9cDbaDd8C8aaDa6Dc4C7cfD37C477D07De3CbcaD7bCcdbD6bC8a6D5cC6adD29C355D0bDe7Cab7D3cC7abD94Db2C8a9D8aC8cdD58C477D08De4Cbd8D4bC9dfD3aC799DaaDc8C9aaDabDc9C7bcDa4Dc2C8aaD8cC7cfD38C477D06De2CcdaD59CacbD88C9b7D4cC6beD49D86Cbc9D5aCcecD78Cbc8D79C5adD28C7cfD47CbdaD6aCbccD34D52C898D7cC5aeD46D56Cab8D5bC8a9D8bCcc9D69C9efD77C6bdD2aC8baD89C7dfD48CddaD3bCbeeD4aC8dfD67" {
    if(isKeyDown("shift"))
	{	run("Z Project...", "projection=[Standard Deviation]");}
	if(isKeyDown("space"))
	{	run("Z Project...", "projection=[Average Intensity]");}
	if(isKeyDown("alt"))
	{	run("Z Project...", "projection=[Sum Slices]");}
	else
    {run("Z Project...", "start=1 stop="+nSlices+" projection=[Max Intensity]");}
}

// Weka Segmentation tool STILL NEED TO ADD
macro "Trained Weka Segmentation Action Tool (+shift to train) - Cb7fD57D76Cc7fD00D01D02D03D04D05D06D07D08D09D0aD0dD0eD0fD10D11D12D13D14D15D16D17D18D19D1aD1dD1eD1fD20D21D22D23D24D25D26D27D28D29D2aD2dD2eD2fD30D31D32D33D34D35D36D37D38D39D3dD3eD3fD40D41D42D43D44D4eD4fD50D51D52D5aD5fD60D61D6fD70D7eD7fD80D8aD8fD90Da0Da1DaaDb0Db1Db2Db3Db7Db8Db9DbaDbbDc0Dc1Dc2Dc3Dc4Dc5Dc6Dc7Dc8Dc9DcaDd0Dd1Dd2Dd3Dd4Dd5Dd6Dd7Dd8Dd9DdeDdfDe0De1De2De3De4De5De6De7DeeDefDf0Df1Df2Df3Df4Df5Df6DfbDfeDffCc7fCa43DbcCb42D85Cd48D3aD71De8C7d7D6dD82Cb43D92C8a8D6bD9eC984Cc42D5eDecCb7eD1cDcbDebCc52D45C9abD3cCc43Da6DfcCb43D2cD62DadDf7Cc6dDb4DdaDeaCc52D56C7d7C7c6D3bD4dDfdCc42D2bCb8eD73DdcDfaCb63D0cDa9De9C9acDedDf9Cb43D99Cb43D0bD8eD9fCb78Cc42D6eDb6DdbC7d8D1bDb5C8a5Cc7eCb63D5bD5cDa2Da5DccC7cbDacCb45DddCa9dCc52C7daDbdC7c7D9bDf8Cb9eD47DbeC9adD7cDa4Ca34D46Cd5aD53Cc43C7d8D72C985D91Cb8fCb53D81C8bbDabDcfCa73D9dDcdCa8dD63D8dCb52D48D49D4bD7bC7d9C7d7C8bcD55DceCb43Cb7bC7d8C8a6Da7Cc7fD4cDa8C8cbCc55D54Ca9eCc53DafC7daD8bD9cC7d7DaeCa9eCaadD7dCc68D4aC9aaC994Cb7fDbfC8bcCb53Cb7dC7d9Da3C7c7C9bcCb7aC7b5Cc7eC7daD8cCd46Ca9dC7daCd5cC7caC985Cc53D5dC9bcCa74Cb8dD9a" {
	
}

// ROI Multimeasure
macro "ROI Multimeasure Tool - C037T0b11RT6b09OTcb09I" {
	img = getTitle()
	run("Set Measurements...", "mean redirect=None decimal=6");
	roiManager("Multi Measure one");
	results = getTitle()
	rename(img+"_results")
}

// Stack Normalization Tool
macro "Stack Normalization Action Tool - 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" {
	runMacro("StackNormalizationTool")
}

// imageCalculator tool
macro "imageCalculator Action Tool - C999D36D37D38Db6Db7Db8C777D5bD5cD5dD65D75D7bD7cD7dD85D9bD9cD9dCfffD00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD10D11D12D13D14D15D16D17D18D19D1aD1bD1cD1dDd0Dd1Dd2Dd3Dd4Dd5Dd6Dd7Dd8Dd9DdaDdbDdcDddDe0De1De2De3De4De5De6De7De8De9DeaDebDecDedDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDffC777D21D22D23D30D35D40D45D48D4aD4eD50D55D60D68D6aD6eD70D80D88D8aD8eD90D95Da0Da5Da8DaaDaeDb0Db5Dc1Dc2Dc3CaaaD4dD6dD8dDacDadC595Da3C666D27D28D29D62D72D82D92Dc7Dc8Dc9C8b8D63D73Db4C888D3cD3dD3eD58D59D5aD5eD78D79D7aD7eD98D99D9aD9eDbcDbdDbeCbbbD47D67D87Da7C888D39D3aD3bD46D56D57D66D76D77D86D96D97Da6Db9DbaDbbC555D2cD32DccCaaaD31D41D51D61D71D81D91Da1Db1CadaD54C8b8D93Db3C666D24D25D26D4cD6cD8cDc4Dc5Dc6C9c9D33D94CeeeD0fD1eDdeDefC444D2eDceC999D20Dc0CbbbD49D4bD69D6bD89D8bDa9DabC696Da4C8c8D43D53CdddD1fDdfC555D2aD2bD2fD42D52Da2Db2DcaDcbDcfCadaD44C8b8D83C9c9D84CfffD0eDeeC444D2dDcdCadaD34C9c9D74C9d9D64" {
	run("Image Calculator...");
}

// Calculator Plus Tool
macro "CalculatorPlus Action Tool - CcccD20D3aD3bD3cD3eD4aD4cD4eD57D58D59D6aD6cD6eD77D78D79D8aD8cD8eD97D98D99DaaDaeDc0C888D2eD4bD4dD6bD6dD8bD8dCfffD00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD10D11D12D13D14D15D16D17D18D19D1aD1bD1cD1dDd0Dd1Dd2Dd3Dd4Dd5Dd6Dd7Dd8De0De1De2De3De4De5De6De7De8De9DeaDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfeDffC182DadCdddD36D37Db6Db7C8c8D43D53C777D3fD4fD5fD6fD7fD8fD9fDafCdddD1fD38D39D46D48D56D66D68D76D86D88D96Da6Da8Db8C8b8D93Db3C3b4DdaDdbDebCeeeD0fD1eD31Db1DefCcccD3dD5aD5bD5cD5eD7aD7bD7cD7eD9aD9eC666D24Dc4C999D2cD47D67D87Da7C3a3DddDedCeeeD41D51D61D71D81D91Da1CbbbD21D30D40D50D5dD60D70D7dD80D90Da0Db0Dc1CaaaD26D27D28Dc6Dc7Dc8C4a5D9bCfffD0eDeeC555D23Dc3C999D2dD2fD49D69D89Da9C293D9cC9c9D74CaaaD29D2aD2bC4e5DacDbcDccDdcDecC777D25D35D45D55D65D75D85D95Da5Db5Dc5C585DdfC6c7DfbC555D22D32D42D52D62D72D82D92Da2Db2Dc2C293DbeC9c9D33D94C8b8D63D73Db4C1d2DceC2a3DbaC5b5Db9C2a3DbbCadaD54C595Da3C5e6DcbC363DbfC192DabC8b8D83C293DbdC9d9D64C4a5D9dC6c7Dd9C293DdeC9c9D84C2e3DcdC3a4DfcC6b6DfdC2a3Dc9CadaD44C696Da4C6e7DcaCadaD34" {
	run("Calculator Plus");
}

// Export as GIF tool
macro "Export GIF Action Tool - C037T0b11GT6b09iTcb09F" {
	img = getTitle()
	path = getInfo("image.directory")
	n = nSlices
	run("Animation Options...", "speed=30 first=1 last=&n");
	run("Series Labeler", "stack_type=[time series or movie] label_format=[Custom Format] custom_suffix=sec custom_format=[] label_unit=[Custom Suffix] decimal_places=1 startup=0.000000000 interval=1.000000000 every_n-th=1 first=0 last=&n location_presets=[Lower Left] x_=0 y_=502");
	run("Duplicate...", "duplicate");
	run("RGB Color");
	saveAs("Gif", path+img+".gif");
}