source: branches/4.2/components/loci-plugins/src/loci/plugins/in/importer-options.txt @ 6669

Revision 6669, 13.8 KB checked in by curtis, 10 years ago (diff)

Backport recent LOCI plugins progress to 4.2 branch.

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[series]
177type = string
178label = series
179default = 0
180
181[showMetadata]
182type = boolean
183label = Display_metadata in results window
184info = <b>Display metadata in results window</b> - \
185  Reads metadata that may be contained within the file format and      \
186  displays it. You can save it as a text file or copy it from the File \
187  and Edit menus specific to the ImageJ Results window. Readability    \
188  depends upon the manner in which metadata is formatted in the data   \
189  source.
190default = false
191
192[showOMEXML]
193type = boolean
194label = Display_OME-XML metadata
195info = <b>Display OME-XML metadata</b> - \
196  Displays a tree of metadata standardized into the OME data model.     \
197  This structure is the same regardless of file format, though some     \
198  formats will populate more information than others.                   \
199  <br><br><b>Examples:</b><ul>                                          \
200  <li>The title of the dataset is listed under                          \
201  OME &gt; Image &gt; Name.</li>                                        \
202  <li>The time and date when the dataset was acquired is listed under   \
203  OME &gt; Image &gt; CreationDate.</li>                                \
204  <li>The physical pixel sizes of each plane in microns is listed under \
205  OME &gt; Image &gt; Pixels &gt;                                       \
206  PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ.</li>                     \
207  </ul>
208default = false
209
210[showROIs]
211type = boolean
212label = Display_ROIs
213info = <b>Display ROIs</b> - \
214  Adds any ROIs in the file to ImageJ's ROI manager.
215default = false
216
217[specifyRanges]
218type = boolean
219label = Specify_range for each series
220info = <b>Specify range for each series</b> - \
221  Opens only the specified range of image planes from a dataset.       \
222  <br><br>After analyzing the dataset dimensional parameters,          \
223  Bio-Formats will present an additional dialog box prompting for the  \
224  desired range.                                                       \
225  <br><br><b>Example:</b> You only want to open the range of focal     \
226  planes in a z-series that actually contain structures of interest to \
227  conserve memory.
228default = false
229
230[splitFocalPlanes]
231type = boolean
232label = Split_focal planes
233info = <b>Split focal planes</b> - \
234  Each focal plane is opened as a separate stack.
235default = false
236
237[splitTimepoints]
238type = boolean
239label = Split_timepoints
240info = <b>Split timepoints</b> - \
241  Timelapse data will be opened as a separate stack for each timepoint.
242default = false
243
244[splitWindows]
245type = boolean
246label = Split_channels
247info = <b>Split channels</b> - \
248  Each channel is opened as a separate stack.                       \
249  <br><br>This option is especially useful if you want to merge the \
250  channels into a specific order, rather than automatically assign  \
251  channels to the order of RGB. The bit depth is preserved.
252default = false
253
254[stackFormat]
255type = string
256label = View stack with:
257info = <b>View stack with</b> - \
258  The type of image viewer to use when displaying the dataset.        \
259  <br><br>Possible choices are:<ul>                                   \
260  <li><b>Metadata only</b> - Display no pixels, only metadata.</li>   \
261  <li><b>Standard ImageJ</b> - Display the pixels in ImageJ's         \
262  built-in 2D viewer.</li>                                            \
263  <li><b>Hyperstack</b> - Display the pixels in ImageJ's              \
264  built-in 5D viewer.</li>                                            \
265  <li><b>Data Browser</b> - Display the pixels in LOCI's              \
266  multidimensional Data Browser viewer. The Data Browser has some     \
267  additional features on top of the normal ImageJ hyperstack.</li>    \
268  <li><b>Image5D</b> - Display the pixels in                          \
269  Joachim Walter's Image5D viewer. Requires the Image5D plugin.</li>  \
270  <li><b>View5D</b> - Display the pixels in                           \
271  Rainer Heintzmann's View5D viewer. Requires the View5D plugin.</li> \
272  </ul>
273default = Hyperstack
274values = \
275  Metadata only,   \
276  Standard ImageJ, \
277  Hyperstack,      \
278  Data Browser,    \
279  Image5D,         \
280  View5D
281
282[stackOrder]
283type = string
284label = Stack_order:
285info = <b>Stack order</b> - \
286  Controls the rasterization order of the dataset's dimensional axes.  \
287  <br><br>Unless you care about the order in which the image planes    \
288  appear, you probably don't need to worry too much about this option. \
289  <br><br>By default, Bio-Formats reads the image planes in whatever   \
290  order they are stored, which is format-dependent. However, several   \
291  stack view modes require a specific rasterization order:<ul>         \
292  <li>Hyperstacks must be in XYCZT order.</li>                         \
293  <li>Image5D must be in XYCZT order.</li>                             \
294  <li>View5D must be in XYZCT order.</li>                              \
295  </ul><b>Example:</b> For a dataset in XYCZT order with 2 channels,   \
296  3 focal planes and 5 time points, the order would be:<ol>            \
297  <li>C1-Z1-T1</li>                                                    \
298  <li>C2-Z1-T1</li>                                                    \
299  <li>C1-Z2-T1</li>                                                    \
300  <li>C2-Z2-T1</li>                                                    \
301  <li>C1-Z3-T1</li>                                                    \
302  <li>C2-Z3-T1</li>                                                    \
303  <li>C1-Z1-T2</li>                                                    \
304  <li>C2-Z1-T2</li>                                                    \
305  <li>etc.</li>                                                        \
306  </ol>
307default = XYCZT
308values = \
309  Default, \
310  XYZCT,   \
311  XYZTC,   \
312  XYCZT,   \
313  XYTCZ,   \
314  XYCTZ,   \
315  XYTZC
316
317[swapDimensions]
318type = boolean
319label = Swap_dimensions
320info = <b>Swap dimensions</b> - \
321  Allows reassignment of dimensional axes (e.g., channel, Z and time).        \
322  <br><br>Bio-Formats is supposed to be smart about handling multidimensional \
323  image data, but in some cases gets things wrong. For example, when          \
324  stitching together a dataset from multiple files using the <b>Group files   \
325  with similar names</b> option, Bio-Formats  may not know which dimensional  \
326  axis the file numbering is supposed to represent. It will take a guess, but \
327  in case it guesses wrong, you can use <b>Swap dimensions</b> to reassign    \
328  which dimensions are which.
329default = false
330
331[upgradeCheck]
332type = boolean
333label = Check_for_upgrades to the LOCI plugins
334default = true
335
336[virtual]
337type = boolean
338label = Use_virtual_stack
339info = <b>Use virtual stack</b> - \
340  Only reads one image plane into memory at a time, loading from the  \
341  data source on the fly as the active image plane changes.           \
342  <br><br>This option is essential for datasets too large to fit into \
343  memory.
344default = false
345
346[windowless]
347type = boolean
348label = windowless
349default = false
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