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        "author": "Dan MacLean",
        "author_email": "dan.maclean@tsl.ac.uk",
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        "description": "===========\nFluorSeg\n===========\n\nFlourSeg provides such and such and so and so. You might find\nit most useful for tasks involving <x> and also <y>. Typical usage\noften looks like this::\n\n    #!/usr/bin/env python\n\n    from fluorseg import liffile\n    from fluorseg import roifile\n\n    lif = liffile.LIFFile(path)\n\n    #show the path\n    print(lif.path)\n\n    #show the metadata xml object\n    print(lif.xml_root)\n\n    #show the number of images in the file\n    print(lif.img_count)\n\n    #show the number of layers in each zstack for each image\n    print(lif.z_stack_count)\n\n    #show the first image's, 2nd zstack layer\n    print(type(lif.combined_channel_images[0][1]))\n\n    #show the type first channel of the first image's 2nd z-stack layer - each data array is a numpy ndarray\n    # they are held in nested lists => [image index][z_stack index]\n    print(type(lif.channel_one_images[0][1]))\n\n    #plot the second channel of the first image's 1st z-stack layer [image index][z_stack index]\n    plt.imshow(lif.channel_two_images[0][0], interpolation='nearest')\n    plt.show()\n\n    #get the maximum projection of each images z-stack for each image\n    max_projs_channel_one = [liffile.max_proj(z_stacks) for z_stacks in lif.channel_one_images]\n    max_projs_channel_two = [liffile.max_proj(z_stacks) for z_stacks in lif.channel_two_images]\n\n    #plot the first max_proj\n    plt.imshow(max_projs_channel_one[0], interpolation='nearest')\n    plt.show()\n\n    plt.imshow(max_projs_channel_two[0], interpolation='nearest')\n    plt.show()\n\n    #get the region of interest info\n    roi_info = roifile.ROIFile(roi_zip_path) #roi for series 001 only\n\n    #make the mask for the second region of interest - a polygon\n    mask = make_polygon_mask(roi_info.rois[1], 512, 512)\n\n    #make the mask for the 5th region of interest - an ellipse\n    oval_mask = make_oval_mask(roi_info.rois[4], 512,512)\n\n    #just get the volume in a region of interest - masking done for you\n    series1_mp_c2 = max_projs_channel_two[0]\n    get_region_volume(series1_mp_c2, roi_info.rois[4])\n\n\n\n(Note the double-colon and 4-space indent formatting above.)\n\nParagraphs are separated by blank lines. *Italics*, **bold**,\nand ``monospace`` look like this.\n\n\nA Section\n=========\n\nLists look like this:\n\n* First\n\n* Second. Can be multiple lines\n  but must be indented properly.\n\nA Sub-Section\n-------------\n\nNumbered lists look like you'd expect:\n\n1. hi there\n\n2. must be going\n\nUrls are http://like.this and links can be\nwritten `like this <http://www.example.com/foo/bar>`_.",
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