QuickStart

1. A text file listing the location of the stitched images needs to be created. e.g. If data were stitched with StitchIt then use generate_MaSIV_list from that package: First cd to the data directory in MATLAB and then run generate_MaSIV_list('stitchedImages_100')or whatever the directory name is for your stitched images.
2. From the MATLAB command line run 'masiv'
3. With the GUI windows that pops up, select the base path of the stitched experiment you would like to view. This is the directory that contains the master Mosaic file, the stitched images sub-directory, and the text files you made in the first step.
4. If you have already run MaSIV on this data set you will be able to select the down-sampled stack to work with.
5. If you have not previously run MaSIV you will need to generate a down-sampled stack. This is done as follows:

• Select 'New'
• Select the channel (these appear by virtue of the text files you generated)
• Specify which slices to use. For example, to use every 3rd slice (in an experiment with 3000 slices), the correct settings would be 1, 3, 3000
• Specify downsampling factor in XY. 10 works nicely for data acquired at 0.5 microns per pixel. A reasonable starting point would be a downsampling factor that will reduce the size of the images to one roughly the number of pixels on your monitor. If the stitched images are 10,000 pixels wide, and your monitor has 1600x1200 pixels, a factor of 6-7 would be about right.
• The downsampled stack will be created and saved to disk, then the viewer will open.

Generating a YML for your data

Should you have a different data set that needs a YML file and so forth, the file itself should be like this:

VoxelSize:
    x: 1
    y: 1
    z: 9

stackName: YH280
imageBaseDirectory: ../

Then the image file list like this:

stitchedImages_100/1/section_001_01.tif
stitchedImages_100/1/section_001_02.tif
stitchedImages_100/1/section_001_03.tif
stitchedImages_100/1/section_001_04.tif
stitchedImages_100/1/section_001_05.tif
stitchedImages_100/1/section_002_01.tif
stitchedImages_100/1/section_002_02.tif
stitchedImages_100/1/section_002_03.tif

The file names of the images don't matter, they just need to be listed. The file name of the list file matters. e.g. it should be: YH280_ImageList_Ch01.txt Here the data structure is:

expRootDir/stitchedImages_100
expRootDir/MASIV_DIR/ymlfile.yml
expRootDir/MASIV_DIR/XXX_ImageList_Ch0X.txt