# Configuration options for Bio-Formats Importer plugin.

[autoscale]
type = boolean
label = Autoscale
info = <b>Autoscale</b> - \
  Stretches the channel histograms to each channel's                   \
  global minimum and maximum value throughout the stack.               \
  Does not alter underlying values in the image.                       \
  <br><br>If unselected, all channel histograms are scaled to the      \
  image's digitization bit depth.                                      \
  Note that this range may be narrower than the bit depth of the file. \
  For example, a 16-bit file may contain intensities digitized to      \
  16-bits (0-65,535), to 12-bits (0-4,095), to 10-bits (0-1,023), etc. \
  <br><br>Note that you can use the Brightness &amp; Contrast or       \
  Window/Level controls to adjust the contrast range regardless of     \
  whether this option is used.                                         \
  The histogram will provide min/max values in the stack.
default = true

[colorMode]
type = string
label = Color_mode:
info = <b>Color mode</b> - \
  Visualizes channels according to the specified scheme.                 \
  <br><br>Possible choices are:<ul>                                      \
  <li><b>Default</b> - Display channels as closely as possible           \
  to how they are stored in the file.</li>                               \
  <li><b>Composite</b> - Open as a merged composite image. Channels are  \
  colorized according to metadata present in the dataset (if any),       \
  or in the following default order: 1=red, 2=green, 3=blue,             \
  4=gray, 5=cyan, 6=magenta, 7=yellow.</li>                              \
  <li><b>Colorized</b> - Open with each channel in a separate plane,     \
  colorized according to metadata present in the dataset (if any),       \
  or in the default order (see Composite above).</li>                    \
  <li><b>Grayscale</b> - Open with each channel in a separate plane,     \
  displayed in plain grayscale.</li>                                     \
  <li><b>Custom</b> - Same as Colorized, except that you                 \
  can explicitly choose how to colorize each channel.</li>               \
  </ul>                                                                  \
  Note that ImageJ can only composite together 7 or fewer channels.      \
  With more than 7 channels, some of the modes above may not work.
default = Default
values = \
  Default,   \
  Composite, \
  Colorized, \
  Grayscale, \
  Custom

[concatenate]
type = boolean
label = Concatenate_series when compatible
info = <b>Concatenate series when compatible</b> - \
  Allows multiple image series to be joined end to end.   \
  <br><br><b>Example:</b> You want to join two sequential \
  timelapse series.
default = false

[crop]
type = boolean
label = Crop on import
info = <b>Crop on import</b> - \
  Image planes may be cropped during import to conserve memory.          \
  <br><br>A window is opened with display of the pixel width and height  \
  of the image plane. Enter the X and Y coordinates for the upper left   \
  corner of the crop region and the width and height of the selection to \
  be displayed, in pixels.
default = false

[firstTime]
type = boolean
default = true

[forceThumbnails]
type = boolean
save = false
label = Force thumbnails
default = false

[groupFiles]
type = boolean
label = Group_files with similar names
info = <b>Group files with similar names</b> - \
  Parses filenames in the selected folder to open files with similar     \
  names as planes in the same dataset.                                   \
  <br><br>The base filename and path is presented before opening for     \
  editing.                                                               \
  <br><br><b>Example:</b> Suppose you have a collection of 12 TIFF files \
  numbered data1.tif, data2.tif, ..., data12.tif, with each file         \
  representing one timepoint, and containing the 9 focal planes at that  \
  timepoint. If you leave this option unchecked and attempt to import    \
  data1.tif, Bio-Formats will create an image stack with 9 planes.       \
  But if you enable this option, Bio-Formats will automatically detect   \
  the other similarly named files and present a confirmation dialog with \
  the detected file pattern, which in this example would be              \
  <code>data&lt;1-12&gt;.tif</code>. You can then edit the pattern in    \
  case it is incorrect. Bio-Formats will then import all 12 x 9 = 108    \
  planes of the dataset.
default = false

[ungroupFiles]
type = boolean
label = Open_files individually
info = <b>Open files individually</b> - \
  Treats each file as an individual file, instead of attempting to group \
  it together with other files that belong to a larger dataset.
default = false

[id]
type = string
label = Open
save = false

[location]
type = string
save = false
default = Local machine
values = \
  Local machine, \
  Internet

[openAllSeries]
type = boolean
label = Open_all_series
info = <b>Open all series</b> - \
  Opens every available image series without prompting.                  \
  <br><br>Some datasets contain multiple distinct image series. Normally \
  when Bio-Formats detects such data it presents a dialog box with       \
  thumbnails allowing individual selection of each available series.     \
  Checking this box instructs Bio-Formats to bypass this dialog box and  \
  instead open every available image series. Essentially, it is a        \
  shortcut for checking all the boxes in the series selector dialog box. \
  It is also useful in a macro when the number of available image series \
  is unknown.
default = false

[quiet]
type = boolean
save = false
label = Quiet mode
default = false

#[record]
#type = boolean
#label = Record_modifications_to_virtual_stack
#info = <b>Record modifications to virtual stack</b> - \
#  <i>BETA FEATURE</i> - Record and reapply changes to virtual stack      \
#  planes.                                                                \
#  <br><br>When viewing as a virtual stack with this option enabled,      \
#  Bio-Formats will attempt to record the operations you perform. When    \
#  you switch to a new image plane, Bio-Formats will "play back" those    \
#  same operations, so that the image plane undergoes the same processing \
#  you performed previously. In this way, the image stack should behave   \
#  more like a normal, fully memory-resident image stack.
#default = false

[showMetadata]
type = boolean
label = Display_metadata
info = <b>Display metadata</b> - \
  Reads metadata that may be contained within the file format and      \
  displays it. You can save it as a text file or copy it from the File \
  and Edit menus specific to the "Original Metadata" window.           \
  Readability depends upon the manner in which metadata is formatted   \
  in the data source. The metadata can also be displayed by pressing   \
  "i" (Image &gt; Show Info) when the imported image is active.
default = false

[showOMEXML]
type = boolean
label = Display_OME-XML metadata
info = <b>Display OME-XML metadata</b> - \
  Displays a tree of metadata standardized into the OME data model.     \
  This structure is the same regardless of file format, though some     \
  formats will populate more information than others.                   \
  <br><br><b>Examples:</b><ul>                                          \
  <li>The title of the dataset is listed under                          \
  OME &gt; Image &gt; Name.</li>                                        \
  <li>The time and date when the dataset was acquired is listed under   \
  OME &gt; Image &gt; CreationDate.</li>                                \
  <li>The physical pixel sizes of each plane in microns is listed under \
  OME &gt; Image &gt; Pixels &gt;                                       \
  PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ.</li>                     \
  </ul>
default = false

[showROIs]
type = boolean
label = Display_ROIs
info = <b>Display ROIs</b> - \
  Adds any ROIs in the file to ImageJ.
default = false

[roiMode]
label = ROIs_Import Mode:
info = <b>ROI Import Mode</b> - \
  ROIs can be imported to the ROI manager or an overlay.
type = string
default = ROI manager
values = \
  ROI manager, \
  Overlay

[specifyRanges]
type = boolean
label = Specify_range for each series
info = <b>Specify range for each series</b> - \
  Opens only the specified range of image planes from a dataset.       \
  <br><br>After analyzing the dataset dimensional parameters,          \
  Bio-Formats will present an additional dialog box prompting for the  \
  desired range.                                                       \
  <br><br><b>Example:</b> You only want to open the range of focal     \
  planes in a z-series that actually contain structures of interest to \
  conserve memory.
default = false

[splitFocalPlanes]
type = boolean
label = Split_focal planes
info = <b>Split focal planes</b> - \
  Each focal plane is opened as a separate stack.
default = false

[splitTimepoints]
type = boolean
label = Split_timepoints
info = <b>Split timepoints</b> - \
  Timelapse data will be opened as a separate stack for each timepoint.
default = false

[splitWindows]
type = boolean
label = Split_channels
info = <b>Split channels</b> - \
  Each channel is opened as a separate stack.                       \
  <br><br>This option is especially useful if you want to merge the \
  channels into a specific order, rather than automatically assign  \
  channels to the order of RGB. The bit depth is preserved.
default = false

[stackFormat]
type = string
label = View stack with:
info = <b>View stack with</b> - \
  The type of image viewer to use when displaying the dataset.        \
  <br><br>Possible choices are:<ul>                                   \
  <li><b>Metadata only</b> - Display no pixels, only metadata.</li>   \
  <li><b>Standard ImageJ</b> - This option is deprecated (i.e.        \
  intended for use by old macros only). Please use <i>Hyperstack</i>  \
  instead.</li>                                                       \
  <li><b>Hyperstack</b> - Display the pixels in ImageJ's              \
  built-in 5D viewer.</li>                                            \
  <li><b>Data Browser</b> - Display the pixels in the                 \
  multidimensional Data Browser viewer. The Data Browser has some     \
  additional features on top of the normal ImageJ hyperstack.</li>    \
  <li><b>Image5D</b> - Display the pixels in                          \
  Joachim Walter's Image5D viewer. Requires the Image5D plugin.</li>  \
  <li><b>View5D</b> - Display the pixels in                           \
  Rainer Heintzmann's View5D viewer. Requires the View5D plugin.</li> \
  </ul>
default = Hyperstack
values = \
  Metadata only,   \
  Standard ImageJ, \
  Hyperstack,      \
  Data Browser,    \
  Image5D,         \
  View5D

[stackOrder]
type = string
label = Stack_order:
info = <b>Stack order</b> - \
  Controls the rasterization order of the dataset's dimensional axes.  \
  <br><br>Unless you care about the order in which the image planes    \
  appear, you probably don't need to worry too much about this option. \
  <br><br>By default, Bio-Formats reads the image planes in whatever   \
  order they are stored, which is format-dependent. However, several   \
  stack view modes require a specific rasterization order:<ul>         \
  <li>Hyperstacks must be in XYCZT order.</li>                         \
  <li>Image5D must be in XYCZT order.</li>                             \
  <li>View5D must be in XYZCT order.</li>                              \
  </ul><b>Example:</b> For a dataset in XYCZT order with 2 channels,   \
  3 focal planes and 5 time points, the order would be:<ol>            \
  <li>C1-Z1-T1</li>                                                    \
  <li>C2-Z1-T1</li>                                                    \
  <li>C1-Z2-T1</li>                                                    \
  <li>C2-Z2-T1</li>                                                    \
  <li>C1-Z3-T1</li>                                                    \
  <li>C2-Z3-T1</li>                                                    \
  <li>C1-Z1-T2</li>                                                    \
  <li>C2-Z1-T2</li>                                                    \
  <li>etc.</li>                                                        \
  </ol>
default = XYCZT
values = \
  Default, \
  XYZCT,   \
  XYZTC,   \
  XYCZT,   \
  XYTCZ,   \
  XYCTZ,   \
  XYTZC

[swapDimensions]
type = boolean
label = Swap_dimensions
info = <b>Swap dimensions</b> - \
  Allows reassignment of dimensional axes (e.g., channel, Z and time).        \
  <br><br>Bio-Formats is supposed to be smart about handling multidimensional \
  image data, but in some cases gets things wrong. For example, when          \
  stitching together a dataset from multiple files using the <b>Group files   \
  with similar names</b> option, Bio-Formats  may not know which dimensional  \
  axis the file numbering is supposed to represent. It will take a guess, but \
  in case it guesses wrong, you can use <b>Swap dimensions</b> to reassign    \
  which dimensions are which.
default = false

[upgradeCheck]
type = boolean
label = Check_for_upgrades to the Bio-Formats plugins
default = true

[virtual]
type = boolean
label = Use_virtual_stack
info = <b>Use virtual stack</b> - \
  Only reads one image plane into memory at a time, loading from the  \
  data source on the fly as the active image plane changes.           \
  <br><br>This option is essential for datasets too large to fit into \
  memory.
default = false

[stitchTiles]
type = boolean
label = Stitch_tiles
info = <b>Stitch tiles</b> - \
  Performs very simple stitching of tiles.                                    \
  <br><br>The overlap is assumed to be 0%, and the stage coordinates are used \
  to determine the proper placement of the tiles.  This is useful for         \
  seeing a quick preview of what the stitched image might look like,          \
  but is not a substitute for proper stitching plugins such as the            \
  <a href="http://pacific.mpi-cbg.de/wiki/index.php/Stitching_2D/3D">         \
  2D/3D Stitching plugin</a>.
default = false

[windowless]
type = boolean
label = windowless
default = false

[mustGroup]
type = boolean
label = mustGroup
default = false
