source: branches/4.2/components/loci-plugins/src/loci/plugins/in/importer-options.txt @ 7000

Revision 7000, 13.8 KB checked in by melissa, 9 years ago (diff)

Merged remaining ImageJ plugin changes to 4.2.

Line 
1#
2# importer-options.txt
3#
4
5# LOCI Plugins for ImageJ: a collection of ImageJ plugins including the
6# Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions,
7# Data Browser and Stack Slicer. Copyright (C) 2005-@year@ Melissa Linkert,
8# Curtis Rueden and Christopher Peterson.
9#
10# This program is free software; you can redistribute it and/or modify
11# it under the terms of the GNU General Public License as published by
12# the Free Software Foundation; either version 2 of the License, or
13# (at your option) any later version.
14#
15# This program is distributed in the hope that it will be useful,
16# but WITHOUT ANY WARRANTY; without even the implied warranty of
17# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18# GNU General Public License for more details.
19#
20# You should have received a copy of the GNU General Public License
21# along with this program; if not, write to the Free Software
22# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
23
24# Configuration options for Bio-Formats Importer plugin.
25
26[autoscale]
27type = boolean
28label = Autoscale
29info = <b>Autoscale</b> - \
30  Stretches the histogram of the image planes to fit the data range.    \
31  Does not alter underlying values in the image. If selected, histogram \
32  is stretched for each stack based upon the global minimum and maximum \
33  value throughout the stack.                                           \
34  <br><br>Note that you can use the Brightness &amp; Contrast or        \
35  Window/Level controls to adjust the contrast range regardless of      \
36  whether this option is used.
37default = true
38
39[colorMode]
40type = string
41label = Color_mode:
42info = <b>Color mode</b> - \
43  Visualizes channels according to the specified scheme.                 \
44  <br><br>Possible choices are:<ul>                                      \
45  <li><b>Default</b> - Display channels as closely as possible           \
46  to how they are stored in the file.</li>                               \
47  <li><b>Composite</b> - Open as a merged composite image. Channels are  \
48  colorized according to metadata present in the dataset (if any),       \
49  or in the following default order: 1=red, 2=green, 3=blue,             \
50  4=gray, 5=cyan, 6=magenta, 7=yellow.</li>                              \
51  <li><b>Colorized</b> - Open with each channel in a separate plane,     \
52  colorized according to metadata present in the dataset (if any),       \
53  or in the default order (see Composite above).</li>                    \
54  <li><b>Grayscale</b> - Open with each channel in a separate plane,     \
55  displayed in plain grayscale.</li>                                     \
56  <li><b>Custom</b> - Same as Colorized, except that you                 \
57  can explicitly choose how to colorize each channel.</li>               \
58  </ul>                                                                  \
59  Note that ImageJ can only composite together 7 or fewer channels.      \
60  With more than 7 channels, some of the modes above may not work.
61default = Default
62values = \
63  Default,   \
64  Composite, \
65  Colorized, \
66  Grayscale, \
67  Custom
68
69[concatenate]
70type = boolean
71label = Concatenate_series when compatible
72info = <b>Concatenate series when compatible</b> - \
73  Allows multiple image series to be joined end to end.   \
74  <br><br><b>Example:</b> You want to join two sequential \
75  timelapse series.
76default = false
77
78[crop]
79type = boolean
80label = Crop on import
81info = <b>Crop on import</b> - \
82  Image planes may be cropped during import to conserve memory.          \
83  <br><br>A window is opened with display of the pixel width and height  \
84  of the image plane. Enter the X and Y coordinates for the upper left   \
85  corner of the crop region and the width and height of the selection to \
86  be displayed, in pixels.
87default = false
88
89[firstTime]
90type = boolean
91default = true
92
93[forceThumbnails]
94type = boolean
95save = false
96label = Force thumbnails
97default = false
98
99[groupFiles]
100type = boolean
101label = Group_files with similar names
102info = <b>Group files with similar names</b> - \
103  Parses filenames in the selected folder to open files with similar     \
104  names as planes in the same dataset.                                   \
105  <br><br>The base filename and path is presented before opening for     \
106  editing.                                                               \
107  <br><br><b>Example:</b> Suppose you have a collection of 12 TIFF files \
108  numbered data1.tif, data2.tif, ..., data12.tif, with each file         \
109  representing one timepoint, and containing the 9 focal planes at that  \
110  timepoint. If you leave this option unchecked and attempt to import    \
111  data1.tif, Bio-Formats will create an image stack with 9 planes.       \
112  But if you enable this option, Bio-Formats will automatically detect   \
113  the other similarly named files and present a confirmation dialog with \
114  the detected file pattern, which in this example would be              \
115  <code>data&lt;1-12&gt;.tif</code>. You can then edit the pattern in    \
116  case it is incorrect. Bio-Formats will then import all 12 x 9 = 108    \
117  planes of the dataset.
118default = false
119
120[ungroupFiles]
121type = boolean
122label = Open_files individually
123info = <b>Open files individually</b> - \
124  Treats each file as an individual file, instead of attempting to group \
125  it together with other files that belong to a larger dataset.
126default = false
127
128[id]
129type = string
130label = Open
131save = false
132
133[location]
134type = string
135save = false
136default = Local machine
137values = \
138  Local machine, \
139  Internet
140
141[openAllSeries]
142type = boolean
143label = Open_all_series
144info = <b>Open all series</b> - \
145  Opens every available image series without prompting.                  \
146  <br><br>Some datasets contain multiple distinct image series. Normally \
147  when Bio-Formats detects such data it presents a dialog box with       \
148  thumbnails allowing individual selection of each available series.     \
149  Checking this box instructs Bio-Formats to bypass this dialog box and  \
150  instead open every available image series. Essentially, it is a        \
151  shortcut for checking all the boxes in the series selector dialog box. \
152  It is also useful in a macro when the number of available image series \
153  is unknown.
154default = false
155
156[quiet]
157type = boolean
158save = false
159label = Quiet mode
160default = false
161
162#[record]
163#type = boolean
164#label = Record_modifications_to_virtual_stack
165#info = <b>Record modifications to virtual stack</b> - \
166#  <i>BETA FEATURE</i> - Record and reapply changes to virtual stack      \
167#  planes.                                                                \
168#  <br><br>When viewing as a virtual stack with this option enabled,      \
169#  Bio-Formats will attempt to record the operations you perform. When    \
170#  you switch to a new image plane, Bio-Formats will "play back" those    \
171#  same operations, so that the image plane undergoes the same processing \
172#  you performed previously. In this way, the image stack should behave   \
173#  more like a normal, fully memory-resident image stack.
174#default = false
175
176[showMetadata]
177type = boolean
178label = Display_metadata
179info = <b>Display metadata</b> - \
180  Reads metadata that may be contained within the file format and      \
181  displays it. You can save it as a text file or copy it from the File \
182  and Edit menus specific to the "Original Metadata" window.           \
183  Readability depends upon the manner in which metadata is formatted   \
184  in the data source. The metadata can also be displayed by pressing   \
185  "i" (Image &gt; Show Info) when the imported image is active.
186default = false
187
188[showOMEXML]
189type = boolean
190label = Display_OME-XML metadata
191info = <b>Display OME-XML metadata</b> - \
192  Displays a tree of metadata standardized into the OME data model.     \
193  This structure is the same regardless of file format, though some     \
194  formats will populate more information than others.                   \
195  <br><br><b>Examples:</b><ul>                                          \
196  <li>The title of the dataset is listed under                          \
197  OME &gt; Image &gt; Name.</li>                                        \
198  <li>The time and date when the dataset was acquired is listed under   \
199  OME &gt; Image &gt; CreationDate.</li>                                \
200  <li>The physical pixel sizes of each plane in microns is listed under \
201  OME &gt; Image &gt; Pixels &gt;                                       \
202  PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ.</li>                     \
203  </ul>
204default = false
205
206[showROIs]
207type = boolean
208label = Display_ROIs
209info = <b>Display ROIs</b> - \
210  Adds any ROIs in the file to ImageJ's ROI manager.
211default = false
212
213[specifyRanges]
214type = boolean
215label = Specify_range for each series
216info = <b>Specify range for each series</b> - \
217  Opens only the specified range of image planes from a dataset.       \
218  <br><br>After analyzing the dataset dimensional parameters,          \
219  Bio-Formats will present an additional dialog box prompting for the  \
220  desired range.                                                       \
221  <br><br><b>Example:</b> You only want to open the range of focal     \
222  planes in a z-series that actually contain structures of interest to \
223  conserve memory.
224default = false
225
226[splitFocalPlanes]
227type = boolean
228label = Split_focal planes
229info = <b>Split focal planes</b> - \
230  Each focal plane is opened as a separate stack.
231default = false
232
233[splitTimepoints]
234type = boolean
235label = Split_timepoints
236info = <b>Split timepoints</b> - \
237  Timelapse data will be opened as a separate stack for each timepoint.
238default = false
239
240[splitWindows]
241type = boolean
242label = Split_channels
243info = <b>Split channels</b> - \
244  Each channel is opened as a separate stack.                       \
245  <br><br>This option is especially useful if you want to merge the \
246  channels into a specific order, rather than automatically assign  \
247  channels to the order of RGB. The bit depth is preserved.
248default = false
249
250[stackFormat]
251type = string
252label = View stack with:
253info = <b>View stack with</b> - \
254  The type of image viewer to use when displaying the dataset.        \
255  <br><br>Possible choices are:<ul>                                   \
256  <li><b>Metadata only</b> - Display no pixels, only metadata.</li>   \
257  <li><b>Standard ImageJ</b> - Display the pixels in ImageJ's         \
258  built-in 2D viewer.</li>                                            \
259  <li><b>Hyperstack</b> - Display the pixels in ImageJ's              \
260  built-in 5D viewer.</li>                                            \
261  <li><b>Data Browser</b> - Display the pixels in LOCI's              \
262  multidimensional Data Browser viewer. The Data Browser has some     \
263  additional features on top of the normal ImageJ hyperstack.</li>    \
264  <li><b>Image5D</b> - Display the pixels in                          \
265  Joachim Walter's Image5D viewer. Requires the Image5D plugin.</li>  \
266  <li><b>View5D</b> - Display the pixels in                           \
267  Rainer Heintzmann's View5D viewer. Requires the View5D plugin.</li> \
268  </ul>
269default = Hyperstack
270values = \
271  Metadata only,   \
272  Standard ImageJ, \
273  Hyperstack,      \
274  Data Browser,    \
275  Image5D,         \
276  View5D
277
278[stackOrder]
279type = string
280label = Stack_order:
281info = <b>Stack order</b> - \
282  Controls the rasterization order of the dataset's dimensional axes.  \
283  <br><br>Unless you care about the order in which the image planes    \
284  appear, you probably don't need to worry too much about this option. \
285  <br><br>By default, Bio-Formats reads the image planes in whatever   \
286  order they are stored, which is format-dependent. However, several   \
287  stack view modes require a specific rasterization order:<ul>         \
288  <li>Hyperstacks must be in XYCZT order.</li>                         \
289  <li>Image5D must be in XYCZT order.</li>                             \
290  <li>View5D must be in XYZCT order.</li>                              \
291  </ul><b>Example:</b> For a dataset in XYCZT order with 2 channels,   \
292  3 focal planes and 5 time points, the order would be:<ol>            \
293  <li>C1-Z1-T1</li>                                                    \
294  <li>C2-Z1-T1</li>                                                    \
295  <li>C1-Z2-T1</li>                                                    \
296  <li>C2-Z2-T1</li>                                                    \
297  <li>C1-Z3-T1</li>                                                    \
298  <li>C2-Z3-T1</li>                                                    \
299  <li>C1-Z1-T2</li>                                                    \
300  <li>C2-Z1-T2</li>                                                    \
301  <li>etc.</li>                                                        \
302  </ol>
303default = XYCZT
304values = \
305  Default, \
306  XYZCT,   \
307  XYZTC,   \
308  XYCZT,   \
309  XYTCZ,   \
310  XYCTZ,   \
311  XYTZC
312
313[swapDimensions]
314type = boolean
315label = Swap_dimensions
316info = <b>Swap dimensions</b> - \
317  Allows reassignment of dimensional axes (e.g., channel, Z and time).        \
318  <br><br>Bio-Formats is supposed to be smart about handling multidimensional \
319  image data, but in some cases gets things wrong. For example, when          \
320  stitching together a dataset from multiple files using the <b>Group files   \
321  with similar names</b> option, Bio-Formats  may not know which dimensional  \
322  axis the file numbering is supposed to represent. It will take a guess, but \
323  in case it guesses wrong, you can use <b>Swap dimensions</b> to reassign    \
324  which dimensions are which.
325default = false
326
327[upgradeCheck]
328type = boolean
329label = Check_for_upgrades to the LOCI plugins
330default = true
331
332[virtual]
333type = boolean
334label = Use_virtual_stack
335info = <b>Use virtual stack</b> - \
336  Only reads one image plane into memory at a time, loading from the  \
337  data source on the fly as the active image plane changes.           \
338  <br><br>This option is essential for datasets too large to fit into \
339  memory.
340default = false
341
342[windowless]
343type = boolean
344label = windowless
345default = false
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