Tool for targeting insertion of microelectrodes based on
brain vasculature, analysing brain vasculature, and 
quantifying damage to vasculature. Still in progress. 

Requirements:
    python, numpy, scipy (0.11.0 or greater), matplotlib

Uses 2-photon microscopy data stored in tif form. Multipage
and singleton series of tifs are supported. 
    
    for multipage : give path to the single file, there 
                    must also be an xml file giving 
                    microscopy metadata by the *same* name
                    except the extension in the *same* folder

    for singleton : give path to the folder containing all
                    tif files for a *single* dataset, the
                    program will default to Ch1 but can be 
                    changed by the -c argument, there must 
                    be an xml file of microscopy metadata 
                    by the *same* name as the folder in 
                    the given folder

TARGETING

Use:

    ./vasc-target path probe-length probe-width

where *path* is the path to the folder with your 2-photon
      tif data and xml metadata file

      *probe-length* is the length of your probe in microns

      *probe-width* is the width of your probe in microns

see ./vasc-target -h for information about options.

Control:

    upon completion of the analysis, a figure will pop up 
    displaying, from left to right and top to bottom, a heat
    map showing the damage value of the least damaging probe
    orientation as well as a marker for the currently 
    selected location, the overall average vasculature image
    as well as a marker for the currently selected position, 
    and a histogram showing the distribution of the damage

        'left'            : choose next location, descending
                            in damage
        'right'           : choose next location, ascending
                            in damage
        'enter'           : choose current location and close
                            window
        'escape'          : close window

Output:

    if you choose a location from the gui, a pdf will be 
    created in current directory displaying the top level
    of imaged vasculature and a marker for the probe location
    chosen -- the naming convention for the pdf is:

        "dam<number of vessels counted>at<y-coord>,<x-coord>.pdf'

STATISTICS

Use:

    ./vasc-stats probe-length probe-width paths ...

where *probe-length* is the length of your probe in microns

      *probe-width* is the width of your probe in microns

      *paths ...* are any number of paths to datasets

see ./vasc-stats -h for information about options.

Output: 

    creates a csv in current directory with various statistics
    about the vasculature -- csv naming convention is:
 
        "stats<time and date of run>.csv"

    with a section for each dataset that was run

DAMAGE QUANTIFICATION

Use:

    ./damage-quant pre post probe-length probe-width

where *pre* is the path to the pre-insertion 2-photon
      tif data

      *post* is the path to the post-insertion 2-photon
      tif data

      *probe-length* is the length of your probe in microns

      *probe-width* is the width of your probe in microns

see ./damage-quant -h for information about options.

Control:

    after the data is read in, a window will pop open with the
    top level of the vasculature images and a probe-image 
    imposed over it; to move the probe image toward the insertion
    location:

        mouse-click       : move probe image to location of click
        'left', 'a', 'j'  : move probe image one pixel left
        'right', 'd', 'l' : move probe image one pixel right
        'up', 'w', 'i'    : move probe image one pixel up
        'down', 's', 'k'  : move probe image one pixel down
        'q'               : rotate probe image one degree 
                            anti-clockwise
        'e'               : rotate probe image one degree 
                            clockwise
        'ctrl+up', 't',   : show slice of data above current
        'ctrl+w'          
        'ctrl+down', 'g', : show slice of data below current
        'ctrl+s'
        'r'               : lock or unlock  probes together across
                            slices

    many keys have multiple options since, depending both on 
    matplotlib backend and operating system, they can be usurped
    for other purposes -- eg, 'ctrl+s' and even 's' are often
    usurped for purposes of saving the figure

Output:

    creates a csv in current directory with side-by-side data
    for pre and post line profiles around chosen point; the 
    rows descend in depth of imaging; the naming convention is:

        "damage<time and date of run>.csv"