README for expNum23_RawData.tar

This contains the raw data for experiment number 23, from 25 August 2015 along with a .csv file containing microscope metadata for each image, and a notes file with notes on the experiment (which may include multiple positions).
Cells were held in glucose for > 24 hours and then switched to galactose and then imaged.
When unzipped, this will have the following structure:

RawData
	> cfpImages
	>	> raw tif files with names cfp_PosX_frameY.tif etc.
	> yfpImages
	> 	> raw tif files with names yfp_PosX_frameY.tif etc.
	> transImages
	> 	> raw tif files with names trans_PosX_frameY.tif etc.
	> a594Images
	>	> raw tif files with names a594_PosX_frameY.tif etc.
	> segmentationImages
	>	> raw tif files with names segZ_PosX_frameY.tif etc.
	> metaInfos_experiment23.csv
	> Notes_2015_08_25_MF_glu-gala.txt

X is the position of the field of view in the microfluidics device. See the experiment name.
Y is the frame number.
Z is the segmentation plane going from below the focal plane to above.

This data was taken on a Nikon TiE microscope in the Rifkin lab at UCSD.

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README for expNum23_ImageAnalysis.tar

This contains the image analysis information for experiment number 23.

When unzipped, this will have the following structure:

ImageAnalysis
	> cellClassification
	>	> localRFClassifier.mat 
		- a matlab .mat file with the random forest used to classify the cells as experimental/control/bad
	> segmentationAndIDMasks
	> 	> files of the form trans_PosX_frameY_UniqID.mat 
		- these are matlab .mat files containing several variables.
			- 'cellMask' is a binary mask of the segmented cells
			- 'parameters' is a struct with parameters used by the segmentation algorithm 
			- 'iChunk' can be ignored
			- 'iFrame' relates to the frame number of the image
			- 'cellMaskLabeled' is again a cell mask, but each segmented object is labeled with its unique identifier in the entire dataset
	> segmentationParameters
	> 	> cellRegionMasks.mat
		-	 a matlab struct called cellRegionMasks which has a mask outlining the region containing cells in the field of view.  Entries are every 25 frames.  Used to eliminate false positives and reduce processing.
	> 	> segmentationParameters1.mat
		- a struct called segPars containing parameters used in th segmentation algorithm. the algorithm considers three sets of parameters
	> 	> segmentationParameters2.mat
	> 	> segmentationParameters3.mat


X is the position of the field of view in the microfluidics device. See the experiment name.
Y is the frame number.

This analysis used Matlab2014a and Matlab2014b.