-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathome.xsd
More file actions
4898 lines (4782 loc) · 255 KB
/
ome.xsd
File metadata and controls
4898 lines (4782 loc) · 255 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<?xml version = "1.0" encoding = "UTF-8"?>
<!--
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Copyright (C) 2002 - 2016 Open Microscopy Environment
# Massachusetts Institute of Technology,
# National Institutes of Health,
# University of Dundee,
# University of Wisconsin at Madison
#
# This work is licensed under the
# Creative Commons Attribution 3.0 Unported License.
# To view a copy of this license, visit
# http://creativecommons.org/licenses/by/3.0/
# or send a letter to
# Creative Commons, 444 Castro Street, Suite 900,
# Mountain View, California, 94041, USA.
# For attribution instructions, visit
# http://www.openmicroscopy.org/info/attribution
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-->
<xsd:schema xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06"
targetNamespace="http://www.openmicroscopy.org/Schemas/OME/2016-06"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:OME="http://www.openmicroscopy.org/Schemas/OME/2016-06"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
version="2"
elementFormDefault="qualified">
<xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="http://www.w3.org/2001/xml.xsd"/>
<xsd:annotation>
<xsd:documentation>
Open Microscopy Environment
OME XML Schema June 2016
</xsd:documentation>
</xsd:annotation>
<!-- Main OME element -->
<xsd:element name="OME"> <!-- top level definition -->
<xsd:annotation>
<xsd:documentation>
The OME element is a container for all information objects accessible by OME.
These information objects include descriptions of the imaging experiments
and the people who perform them, descriptions of the microscope, the resulting
images and how they were acquired, the analyses performed on those images,
and the analysis results themselves.
An OME file may contain any or all of this information.
With the creation of the Metadata Only Companion OME-XML and Binary Only OME-TIFF files
the top level OME node has changed slightly.
It can EITHER:
Contain all the previously expected elements
OR:
Contain a single BinaryOnly element that points at
its Metadata Only Companion OME-XML file.
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="Rights" minOccurs="0" maxOccurs="1"/>
<xsd:choice>
<!-- Either: standard expected elements -->
<xsd:sequence>
<xsd:element ref="Project" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="Dataset" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="Folder" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="Experiment" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="Plate" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="Screen" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="Experimenter" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="ExperimenterGroup" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="Instrument" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="Image" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="StructuredAnnotations" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="ROI" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<!-- Or: Single BinaryOnly element -->
<xsd:element name="BinaryOnly" minOccurs="1" maxOccurs="1">
<xsd:annotation>
<xsd:documentation> Pointer to an external metadata file. If this
element is present, then no other metadata may be present in this
file, i.e. this file is a place-holder. </xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:attribute name="MetadataFile" type="xsd:string" use="required">
<xsd:annotation>
<xsd:documentation> Filename of the OME-XML metadata file for
this binary data. If the file cannot be found, a search can
be performed based on the UUID. </xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="UUID" type="UniversallyUniqueIdentifier"
use="required">
<xsd:annotation>
<xsd:documentation> The unique identifier of another OME-XML
block whose metadata describes the binary data in this file.
This UUID is considered authoritative regardless of
mismatches in the filename. </xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<!-- End of MetadataOnly Element -->
</xsd:choice>
</xsd:sequence>
<xsd:attribute name="UUID" type="UniversallyUniqueIdentifier" use="optional">
<xsd:annotation>
<xsd:documentation>
This unique identifier is used to keep track of multi part files.
It allows the links between files to survive renaming.
While OPTIONAL in the general case this is REQUIRED in a
MetadataOnly Companion to a collection of BinaryOnly files.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="Creator" type="xsd:string" use="optional">
<xsd:annotation>
<xsd:documentation>
This is the name of the creating application of the OME-XML
and preferably its full version.
e.g "CompanyName, SoftwareName, V2.6.3456"
This is optional but we hope it will be set by applications
writing out OME-XML from scratch.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
<!-- Unique IDs -->
<xsd:key name="ChannelIDKey"><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="DatasetIDKey"><xsd:selector xpath="OME:Dataset"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="DetectorIDKey"><xsd:selector xpath="OME:Instrument/OME:Detector"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="DichroicIDKey"><xsd:selector xpath="OME:Instrument/OME:Dichroic"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="ExperimentIDKey"><xsd:selector xpath="OME:Experiment"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="ExperimenterIDKey"><xsd:selector xpath="OME:Experimenter"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="FilterIDKey"><xsd:selector xpath="OME:Instrument/OME:Filter"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="FilterSetIDKey"><xsd:selector xpath="OME:Instrument/OME:FilterSet"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="FolderIDKey"><xsd:selector xpath="OME:Folder"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="ExperimenterGroupIDKey"><xsd:selector xpath="OME:ExperimenterGroup"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="ImageIDKey"><xsd:selector xpath="OME:Image"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="InstrumentIDKey"><xsd:selector xpath="OME:Instrument"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="LightSourceIDKey"><xsd:selector xpath="OME:Instrument/OME:Laser|OME:Instrument/OME:Arc|OME:Instrument/OME:Filament|OME:Instrument/OME:LightEmittingDiode|OME:Instrument/OME:GenericExcitationSource"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="MicrobeamManipulationIDKey"><xsd:selector xpath="OME:Experiment/OME:MicrobeamManipulation"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="ObjectiveIDKey"><xsd:selector xpath="OME:Instrument/OME:Objective"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="PixelsIDKey"><xsd:selector xpath="OME:Image/OME:Pixels"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="PlateIDKey"><xsd:selector xpath="OME:Plate"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="ProjectIDKey"><xsd:selector xpath="OME:Project"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="ReagentIDKey"><xsd:selector xpath="OME:Screen/OME:Reagent"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="ScreenAcquisitionIDKey"><xsd:selector xpath="OME:Screen/OME:ScreenAcquisition"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="ScreenIDKey"><xsd:selector xpath="OME:Screen"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="WellIDKey"><xsd:selector xpath="OME:Plate/OME:Well"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="WellSampleIDKey"><xsd:selector xpath="OME:Plate/OME:Well/OME:WellSample"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="ROIIDKey"><xsd:selector xpath="OME:ROI"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="ShapeIDKey"><xsd:selector xpath="OME:ROI/OME:Union/OME:Rectangle|OME:ROI/OME:Union/OME:Mask|OME:ROI/OME:Union/OME:Ellipse|OME:ROI/OME:Union/OME:Point|OME:ROI/OME:Union/OME:Line|OME:ROI/OME:Union/OME:Polyline|OME:ROI/OME:Union/OME:Polygon|OME:ROI/OME:Union/OME:Label"/><xsd:field xpath="@ID"/></xsd:key>
<xsd:key name="AnnotationIDKey"><xsd:selector xpath="OME:StructuredAnnotations/*"/><xsd:field xpath="@ID"/></xsd:key>
<!-- Unique references -->
<xsd:key name="WellSampleImageRefIDKey"><xsd:selector xpath="OME:Plate/OME:Well/OME:WellSample/OME:ImageRef"/><xsd:field xpath="@ID"/></xsd:key>
<!-- Valid references -->
<xsd:keyref name="DatasetExperimenterIDKeyRef" refer="OME:ExperimenterIDKey" ><xsd:selector xpath="OME:Dataset/OME:ExperimenterRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="DatasetExperimenterGroupIDKeyRef" refer="OME:ExperimenterGroupIDKey" ><xsd:selector xpath="OME:Dataset/OME:ExperimenterGroupRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="DatasetProjectIDKeyRef" refer="OME:ProjectIDKey" ><xsd:selector xpath="OME:Dataset/OME:ProjectRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ExperimentExperimenterIDKeyRef" refer="OME:ExperimenterIDKey" ><xsd:selector xpath="OME:Experiment/OME:ExperimenterRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ExperimentMicrobeamManipulationExperimenterIDKeyRef" refer="OME:ExperimenterIDKey" ><xsd:selector xpath="OME:Experiment/OME:MicrobeamManipulation/OME:ExperimenterRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ExperimentMicrobeamManipulationLightSourceSettingsLightSourceIDKeyRef" refer="OME:LightSourceIDKey" ><xsd:selector xpath="OME:Experiment/OME:MicrobeamManipulation/OME:LightSourceSettings"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ExperimenterExperimenterGroupIDKeyRef" refer="OME:ExperimenterGroupIDKey" ><xsd:selector xpath="OME:Experimenter/OME:ExperimenterGroupRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ExperimenterGroupContactExperimenterIDKeyRef" refer="OME:ExperimenterIDKey" ><xsd:selector xpath="OME:ExperimenterGroup/OME:Contact"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ExperimenterGroupLeaderExperimenterIDKeyRef" refer="OME:ExperimenterIDKey" ><xsd:selector xpath="OME:ExperimenterGroup/OME:Leader"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="FolderFolderIDKeyRef" refer="OME:FolderIDKey" ><xsd:selector xpath="OME:Folder/OME:FolderRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="FolderImageIDKeyRef" refer="OME:ImageIDKey" ><xsd:selector xpath="OME:Folder/OME:ImageRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="FolderROIIDKeyRef" refer="OME:ROIIDKey" ><xsd:selector xpath="OME:Folder/OME:ROIRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImageDatasetIDKeyRef" refer="OME:DatasetIDKey" ><xsd:selector xpath="OME:Image/OME:DatasetRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImageExperimenterIDKeyRef" refer="OME:ExperimenterIDKey" ><xsd:selector xpath="OME:Image/OME:ExperimenterRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImageExperimentIDKeyRef" refer="OME:ExperimentIDKey" ><xsd:selector xpath="OME:Image/OME:ExperimentRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImageExperimenterGroupIDKeyRef" refer="OME:ExperimenterGroupIDKey" ><xsd:selector xpath="OME:Image/OME:ExperimenterGroupRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImageInstrumentIDKeyRef" refer="OME:InstrumentIDKey" ><xsd:selector xpath="OME:Image/OME:InstrumentRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImageMicrobeamManipulationIDKeyRef" refer="OME:MicrobeamManipulationIDKey" ><xsd:selector xpath="OME:Image/OME:MicrobeamManipulationRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImageObjectiveSettingsObjectiveIDKeyRef" refer="OME:ObjectiveIDKey" ><xsd:selector xpath="OME:Image/OME:ObjectiveSettings"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImagePixelsChannelDetectorSettingsDetectorIDKeyRef" refer="OME:DetectorIDKey" ><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:DetectorSettings"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImagePixelsChannelFilterSetIDKeyRef" refer="OME:FilterSetIDKey" ><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:FilterSetRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImagePixelsChannelLightPathExcitationFilterIDKeyRef" refer="OME:FilterIDKey" ><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightPath/OME:ExcitationFilterPath/OME:FilterRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImagePixelsChannelLightPathExcitationDichroicIDKeyRef" refer="OME:DichroicIDKey" ><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightPath/OME:ExcitationFilterPath/OME:DichroicRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImagePixelsChannelLightPathDichroicIDKeyRef" refer="OME:DichroicIDKey" ><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightPath/OME:DichroicRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImagePixelsChannelLightPathEmissionFilterIDKeyRef" refer="OME:FilterIDKey" ><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightPath/OME:EmissionFilterPath/OME:FilterRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImagePixelsChannelLightPathEmissionDichroicIDKeyRef" refer="OME:DichroicIDKey" ><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightPath/OME:EmissionFilterPath/OME:DichroicRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImagePixelsChannelLightSourceSettingsLightSourceIDKeyRef" refer="OME:LightSourceIDKey" ><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightSourceSettings"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="InstrumentFilterSetExcitationFilterIDKeyRef" refer="OME:FilterIDKey" ><xsd:selector xpath="OME:Instrument/OME:FilterSet/OME:ExcitationFilterRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="InstrumentFilterSetDichroicIDKeyRef" refer="OME:DichroicIDKey" ><xsd:selector xpath="OME:Instrument/OME:FilterSet/OME:DichroicRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="InstrumentFilterSetEmissionFilterIDKeyRef" refer="OME:FilterIDKey" ><xsd:selector xpath="OME:Instrument/OME:FilterSet/OME:EmissionFilterRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="InstrumentLightSourceLaserPumpLightSourceIDKey" refer="OME:LightSourceIDKey" ><xsd:selector xpath="OME:Instrument/OME:LightSource/OME:Laser/OME:Pump"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="PlateScreenIDKeyRef" refer="OME:ScreenIDKey" ><xsd:selector xpath="OME:Plate/OME:ScreenRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="PlateWellReagentIDKeyRef" refer="OME:ReagentIDKey" ><xsd:selector xpath="OME:Plate/OME:Well/OME:ReagentRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="PlateWellWellSampleImageIDKeyRef" refer="OME:ImageIDKey" ><xsd:selector xpath="OME:Plate/OME:Well/OME:WellSample/OME:ImageRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ProjectExperimenterIDKeyRef" refer="OME:ExperimenterIDKey" ><xsd:selector xpath="OME:Project/OME:ExperimenterRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ProjectExperimenterGroupIDKeyRef" refer="OME:ExperimenterGroupIDKey" ><xsd:selector xpath="OME:Project/OME:ExperimenterGroupRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ScreenPlateIDKeyRef" refer="OME:PlateIDKey" ><xsd:selector xpath="OME:Screen/OME:PlateRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ScreenScreenAcquisitionWellSampleIDKeyRef" refer="OME:WellSampleIDKey" ><xsd:selector xpath="OME:Screen/OME:ScreenAcquisition/OME:WellSampleRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ExperimentMicrobeamManipulationROIIDKeyRef" refer="OME:ROIIDKey" ><xsd:selector xpath="OME:Experiment/OME:MicrobeamManipulation/ROIRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="ImageROIIDKeyRef" refer="OME:ROIIDKey" ><xsd:selector xpath="OME:Image/ROIRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="AnnotationRefAnnotationIDKeyRef" refer="OME:AnnotationIDKey"><xsd:selector xpath=".//OME:AnnotationRef"/><xsd:field xpath="@ID"/></xsd:keyref>
<xsd:keyref name="AnnotationAnnotatorExperimenterIDKeyRef" refer="OME:ExperimenterIDKey"><xsd:selector xpath="OME:StructuredAnnotations/*"/><xsd:field xpath="@Annotator"/></xsd:keyref>
</xsd:element>
<!-- Key pixel storage elements -->
<xsd:element name="Image"> <!-- top level definition -->
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><plural>Images</plural></xsdfu></xsd:appinfo>
<xsd:documentation>
This element describes the actual image and its meta-data.
The elements that are references (ending in Ref or Settings) refer to
elements defined outside of the Image element. Ref elements are simple
links, while Settings elements are links with additional values.
If any of the required Image attributes or elements are missing, its
guaranteed to be an invalid document. The required attributes and
elements are ID and Pixels.
ExperimenterRef is required for all Images with well formed LSIDs.
ImageType is a vendor-specific designation of the type of image this is.
Examples of ImageType include 'STK', 'SoftWorx', etc.
The Name attributes are in all cases the name of the element
instance. In this case, the name of the image, not necessarily the filename.
Physical size of pixels are microns[µm].
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element name="AcquisitionDate" minOccurs="0" maxOccurs="1" type="xsd:dateTime">
<xsd:annotation>
<xsd:documentation>
The acquisition date of the Image.
The element contains an xsd:dateTime string based on the ISO 8601 format (i.e. 1988-04-07T18:39:09.359)
YYYY-MM-DDTHH:mm:SS.sssZ
Y - Year
M - Month
D - Day
H - Hour
m - minutes
S - Seconds
s - sub-seconds (optional)
Z - Zone (optional) +HH:mm or -HH:mm or Z for UTC
Note: xsd:dataTime supports a very wide date range with unlimited precision. The full date range
and precision are not typically supported by platform- and language-specific libraries.
Where the supported time precision is less than the precision used by the xsd:dateTime
timestamp there will be loss of precision; this will typically occur via direct truncation
or (less commonly) rounding.
The year value can be large and/or negative. Any value covering the current or last century
should be correctly processed, but some systems cannot process earlier dates.
The sub-second value is defined as an unlimited number of digits after the decimal point.
In Java a minimum of millisecond precision is guaranteed.
In C++ microsecond precision is guaranteed, with nanosecond precision being available on
some platforms.
Time zones are supported, eg '2013-10-24T11:52:33+01:00' for Paris, but in most cases it will
be converted to UTC when the timestamp is written.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element ref="ExperimenterRef" minOccurs="0" maxOccurs="1"/>
<xsd:element name="Description" minOccurs="0" maxOccurs="1">
<xsd:annotation>
<xsd:documentation>
A description for the image. [plain-text multi-line string]
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:whiteSpace value="preserve"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:element>
<xsd:element ref="ExperimentRef" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="ExperimenterGroupRef" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="InstrumentRef" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="ObjectiveSettings" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="ImagingEnvironment" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="StageLabel" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="Pixels" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="ROIRef" minOccurs="0" maxOccurs="unbounded">
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><manytomany/></xsdfu></xsd:appinfo>
</xsd:annotation>
</xsd:element>
<xsd:element ref="MicrobeamManipulationRef" minOccurs="0" maxOccurs="unbounded">
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><manytomany/></xsdfu></xsd:appinfo>
</xsd:annotation>
</xsd:element>
<xsd:element ref="AnnotationRef" minOccurs="0" maxOccurs="unbounded">
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><manytomany/></xsdfu></xsd:appinfo>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="ID" use="required" type="ImageID"/>
<xsd:attribute name="Name" use="optional" type="xsd:string"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="Pixels"> <!-- top level definition -->
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><plural>Pixels</plural></xsdfu></xsd:appinfo>
<xsd:documentation>
Pixels is going to be removed in the future, but it is still required.
This is just notice that the contents of Pixels will be
moved up to Image in a future release. This is because there
has only been 1 Pixels object in each Image for some time.
The concept of multiple Pixels sets for one Image failed to
take off. It is therefore redundant.
The Image will be unreadable if any of the required Pixel attributes are missing.
The Pixels themselves can be stored within the OME-XML compressed by plane, and encoded
in Base64.
Or the Pixels may be stored in TIFF format.
The Pixels element should contain a list of BinData or TiffData, each containing a
single plane of pixels. These Pixels elements, when read in document order,
must produce a 5-D pixel array of the size specified in this element, and in the
dimension order specified by 'DimensionOrder'.
All of the values in the Pixels object when present should match the same value
stored in any associated TIFF format (e.g. SizeX should be the same). Where there
is a mismatch our readers will take the value from the TIFF structure as overriding
the value in the OME-XML. This is simply a pragmatic decision as it increases the
likelihood of reading data from a slightly incorrect file.
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="Channel" minOccurs="0" maxOccurs="unbounded">
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><ordered/></xsdfu></xsd:appinfo>
</xsd:annotation>
</xsd:element>
<xsd:choice minOccurs="1" maxOccurs="1">
<xsd:element ref="BinData" minOccurs="1" maxOccurs="unbounded"/>
<xsd:element ref="TiffData" minOccurs="1" maxOccurs="unbounded"/>
<xsd:element ref="MetadataOnly" minOccurs="1" maxOccurs="1"/>
</xsd:choice>
<xsd:element ref="Plane" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="ID" use="required" type="PixelsID"/>
<xsd:attribute name="DimensionOrder" use="required">
<xsd:annotation>
<xsd:documentation>
The order in which the individual planes of data are interleaved.
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="XYZCT"/>
<xsd:enumeration value="XYZTC"/>
<xsd:enumeration value="XYCTZ"/>
<xsd:enumeration value="XYCZT"/>
<xsd:enumeration value="XYTCZ"/>
<xsd:enumeration value="XYTZC"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="Type" use="required" type="PixelType">
<xsd:annotation>
<xsd:documentation>
The variable type used to represent each pixel in the image.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="SignificantBits" use="optional" type="PositiveInt">
<xsd:annotation>
<xsd:documentation>
The number of bits within the type storing each pixel that are significant.
e.g. you can store 12 bit data within a 16 bit type.
This does not reduce the storage requirements but can be a useful indicator
when processing or viewing the image data.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="Interleaved" use="optional" type="xsd:boolean">
<xsd:annotation>
<xsd:documentation>
How the channels are arranged within the data block:
true if channels are stored RGBRGBRGB...;
false if channels are stored RRR...GGG...BBB...
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="BigEndian" use="optional" type="xsd:boolean">
<xsd:annotation>
<xsd:documentation>
This is true if the pixels data was written in BigEndian order.
If this value is present it should match the value used in BinData
or TiffData. If it does not a reader should honour the value used
in the BinData or TiffData. This values is useful for MetadataOnly
files and is to allow for future storage solutions.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="SizeX" use="required" type="PositiveInt">
<xsd:annotation>
<xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="SizeY" use="required" type="PositiveInt">
<xsd:annotation>
<xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="SizeZ" use="required" type="PositiveInt">
<xsd:annotation>
<xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="SizeC" use="required" type="PositiveInt">
<xsd:annotation>
<xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="SizeT" use="required" type="PositiveInt">
<xsd:annotation>
<xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PhysicalSizeX" use="optional" type="PositiveFloat">
<xsd:annotation>
<xsd:documentation>Physical size of a pixel. Units are set by PhysicalSizeXUnit.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PhysicalSizeXUnit" use="optional" default="µm" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the physical size of a pixel - default:microns[µm].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PhysicalSizeY" use="optional" type="PositiveFloat">
<xsd:annotation>
<xsd:documentation>Physical size of a pixel. Units are set by PhysicalSizeYUnit.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PhysicalSizeYUnit" use="optional" default="µm" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the physical size of a pixel - default:microns[µm].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PhysicalSizeZ" use="optional" type="PositiveFloat">
<xsd:annotation>
<xsd:documentation>Physical size of a pixel. Units are set by PhysicalSizeZUnit.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PhysicalSizeZUnit" use="optional" default="µm" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the physical size of a pixel - default:microns[µm].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="TimeIncrement" use="optional" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
TimeIncrement is used for time series that have a global
timing specification instead of per-timepoint timing info.
For example in a video stream. Units are set by TimeIncrementUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="TimeIncrementUnit" use="optional" default="s" type="UnitsTime">
<xsd:annotation>
<xsd:documentation>The units of the TimeIncrement - default:seconds[s].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="Plane"> <!-- top level definition -->
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><plural>Planes</plural></xsdfu></xsd:appinfo>
<xsd:documentation>
The Plane object holds microscope stage and image timing data
for a given channel/z-section/timepoint.
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:choice minOccurs="0" maxOccurs="1">
<xsd:annotation>
<xsd:documentation>
This optional element is a hash of the plane's image data.
It is a choice between all the support hash types.
Currently the only method supported is SHA1.
</xsd:documentation>
</xsd:annotation>
<xsd:element name="HashSHA1" type="Hex40" minOccurs="1" maxOccurs="1"/>
</xsd:choice>
<xsd:element ref="AnnotationRef" minOccurs="0" maxOccurs="unbounded">
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><manytomany/></xsdfu></xsd:appinfo>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="TheZ" use="required" type="NonNegativeInt">
<xsd:annotation>
<xsd:documentation>
The Z-section this plane is for. [units:none]
This is numbered from 0.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="TheT" use="required" type="NonNegativeInt">
<xsd:annotation>
<xsd:documentation>
The timepoint this plane is for. [units:none]
This is numbered from 0.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="TheC" use="required" type="NonNegativeInt">
<xsd:annotation>
<xsd:documentation>
The channel this plane is for. [units:none]
This is numbered from 0.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="DeltaT" use="optional" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
Time since the beginning of the experiment.
Units are set by DeltaTUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="DeltaTUnit" use="optional" default="s" type="UnitsTime">
<xsd:annotation>
<xsd:documentation>The units of the DeltaT - default:seconds[s].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="ExposureTime" use="optional" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
The length of the exposure.
Units are set by ExposureTimeUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="ExposureTimeUnit" use="optional" default="s" type="UnitsTime">
<xsd:annotation>
<xsd:documentation>The units of the ExposureTime - default:seconds[s].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PositionX" use="optional" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
The X position of the stage. Units are set by PositionXUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PositionXUnit" use="optional" default="reference frame" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the X stage position - default:[reference frame].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PositionY" use="optional" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
The Y position of the stage. Units are set by PositionYUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PositionYUnit" use="optional" default="reference frame" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the Y stage position - default:[reference frame].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PositionZ" use="optional" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
The Z position of the stage. Units are set by PositionZUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PositionZUnit" use="optional" default="reference frame" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the Z stage position - default:[reference frame].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="Channel"> <!-- top level definition -->
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><plural>Channels</plural></xsdfu></xsd:appinfo>
<xsd:documentation>
There must be one per channel in the Image, even for a single-plane image.
And information about how each of them was acquired is stored in the various optional *Ref elements. Each Logical Channel is composed of one or more
ChannelComponents. For example, an entire spectrum in an FTIR experiment may be stored in a single Logical Channel with each discrete wavenumber of the spectrum
constituting a ChannelComponent of the FTIR Logical Channel. An RGB image where the Red, Green and Blue components do not reflect discrete probes but are
instead the output of a color camera would be treated similarly - one Logical channel with three ChannelComponents in this case.
The total number of ChannelComponents for a set of pixels must equal SizeC.
The IlluminationType attribute is a string enumeration which may be set to 'Transmitted', 'Epifluorescence', 'Oblique', or 'NonLinear'.
The user interface logic for labeling a given channel for the user should use the first existing attribute in the following sequence:
Name -> Fluor -> EmissionWavelength -> ChannelComponent/Index.
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="LightSourceSettings" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="DetectorSettings" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="FilterSetRef" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="AnnotationRef" minOccurs="0" maxOccurs="unbounded">
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><manytomany/></xsdfu></xsd:appinfo>
</xsd:annotation>
</xsd:element>
<xsd:element ref="LightPath" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute name="ID" use="required" type="ChannelID"/>
<xsd:attribute name="Name" use="optional" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
A name for the channel that is suitable for presentation to the user.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="SamplesPerPixel" use="optional" type="PositiveInt">
<xsd:annotation>
<xsd:documentation>
The number of samples the detector takes to form each pixel value. [units:none]
Note: This is not the same as "Frame Averaging" - see Integration in DetectorSettings
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="IlluminationType" use="optional">
<xsd:annotation>
<xsd:documentation>
The method of illumination used to capture the channel.
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="Transmitted"/>
<xsd:enumeration value="Epifluorescence"/>
<xsd:enumeration value="Oblique"/>
<xsd:enumeration value="NonLinear"/>
<xsd:enumeration value="Other"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="PinholeSize" use="optional" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
The optional PinholeSize attribute allows specifying adjustable
pin hole diameters for confocal microscopes. Units are set by PinholeSizeUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PinholeSizeUnit" use="optional" default="µm" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the pin hole diameter for confocal microscopes - default:microns[µm].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="AcquisitionMode" use="optional">
<xsd:annotation>
<xsd:documentation>
AcquisitionMode describes the type of microscopy performed for each channel
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="WideField"/>
<xsd:enumeration value="LaserScanningConfocalMicroscopy"/> <!-- CLSM or LSCM -->
<xsd:enumeration value="SpinningDiskConfocal"/>
<xsd:enumeration value="SlitScanConfocal"/>
<xsd:enumeration value="MultiPhotonMicroscopy"/><!-- laser scanning multiphoton microscopy (LSMM), two photon microscopy -->
<xsd:enumeration value="StructuredIllumination"/>
<xsd:enumeration value="SingleMoleculeImaging"/>
<xsd:enumeration value="TotalInternalReflection"/>
<xsd:enumeration value="FluorescenceLifetime"/>
<xsd:enumeration value="SpectralImaging"/>
<xsd:enumeration value="FluorescenceCorrelationSpectroscopy"/>
<xsd:enumeration value="NearFieldScanningOpticalMicroscopy"/><!-- NSOM -->
<xsd:enumeration value="SecondHarmonicGenerationImaging"/><!-- Second harmonic imaging microscopy (SHIM) -->
<xsd:enumeration value="PALM"/><!-- photo-activated localization microscopy, photo-activation localization microscopy -->
<xsd:enumeration value="STORM"/><!-- stochastic optical reconstruction microscopy -->
<xsd:enumeration value="STED"/><!-- stimulated emission depletion -->
<xsd:enumeration value="TIRF"/><!-- total internal reflection fluorescence (TIRFM) -->
<xsd:enumeration value="FSM"/><!-- Fluorescence speckle microscopy -->
<xsd:enumeration value="LCM"/><!-- Laser capture microdissection -->
<xsd:enumeration value="Other"/>
<xsd:enumeration value="BrightField"/>
<xsd:enumeration value="SweptFieldConfocal"/>
<xsd:enumeration value="SPIM"/><!-- Selective or Single Plane Illumination Microscopy -->
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="ContrastMethod" use="optional">
<xsd:annotation>
<xsd:documentation>
ContrastMethod describes the technique used to achieve contrast for each channel
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="Brightfield"/>
<xsd:enumeration value="Phase"/>
<xsd:enumeration value="DIC"/><!-- Differential Interference Contrast -->
<xsd:enumeration value="HoffmanModulation"/><!-- Hoffman Modulation Contrast (HMC) -->
<xsd:enumeration value="ObliqueIllumination"/>
<xsd:enumeration value="PolarizedLight"/> <!-- Polarization Microscopy -->
<xsd:enumeration value="Darkfield"/><!-- Dark Field Imaging -->
<xsd:enumeration value="Fluorescence"/>
<xsd:enumeration value="Other"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="ExcitationWavelength" use="optional" type="PositiveFloat">
<xsd:annotation>
<xsd:documentation>
Wavelength of excitation for a particular channel. Units are set by ExcitationWavelengthUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="ExcitationWavelengthUnit" use="optional" default="nm" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the wavelength of excitation - default:nanometres[nm].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="EmissionWavelength" use="optional" type="PositiveFloat">
<xsd:annotation>
<xsd:documentation>
Wavelength of emission for a particular channel. Units are set by EmissionWavelengthUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="EmissionWavelengthUnit" use="optional" default="nm" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the wavelength of emission - default:nanometres[nm].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="Fluor" use="optional" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
The Fluor attribute is used for fluorescence images.
This is the name of the fluorophore used to produce this channel [plain text string]
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="NDFilter" use="optional" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
The NDfilter attribute is used to specify the combined effect of any neutral density filters used.
The amount of light the filter transmits at a maximum [units:none]
A fraction, as a value from 0.0 to 1.0.
NOTE: This was formerly described as "units optical density expressed as a PercentFraction".
This was how the field had been described in the schema from the beginning but all
the use of it has been in the opposite direction, i.e. as a amount transmitted,
not the amount blocked. This change has been made to make the model reflect this usage.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PockelCellSetting" use="optional" type="xsd:int">
<xsd:annotation>
<xsd:documentation>
The PockelCellSetting used for this channel. This is the amount the polarization of the beam is rotated by. [units:none]
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="Color" use="optional" type="Color" default="-1">
<xsd:annotation>
<xsd:documentation>
A color used to render this channel - encoded as RGBA
The default value "-1" is #FFFFFFFF so solid white (it is a signed 32 bit value)
NOTE: Prior to the 2012-06 schema the default value was incorrect and produced a transparent red not solid white.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<!-- Other elements associated with pixel storage -->
<xsd:element name="MetadataOnly"> <!-- top level definition -->
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><plural>MetadataOnlyMarkers</plural></xsdfu></xsd:appinfo>
<xsd:documentation>
This place holder means there is on pixel data in this file.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="TiffData"> <!-- top level definition -->
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><plural>TiffDataBlocks</plural></xsdfu></xsd:appinfo>
<xsd:documentation>
This described the location of the pixel data in a tiff file.
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element name="UUID" minOccurs="0" maxOccurs="1">
<xsd:annotation>
<xsd:documentation>
This must be used when the IFDs are located in another file.
Note: It is permissible for this to be self referential.
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base = "UniversallyUniqueIdentifier">
<xsd:attribute name="FileName" use="optional" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
This can be used when the IFDs are located in another file.
The / (forward slash) is used as the path separator.
A relative path is recommended. However an absolute path can be specified.
Default is to use the file the ome-xml data has been pulled from.
Note: It is permissible for this to be self referential. The file image1.tiff
may contain ome-xml data that has FilePath="image1.tiff" or "./image1.tiff"
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="IFD" type="NonNegativeInt" default="0" use="optional">
<xsd:annotation>
<xsd:documentation>
Gives the IFD(s) for which this element is applicable. Indexed from 0.
Default is 0 (the first IFD). [units:none]
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="FirstZ" type="NonNegativeInt" default="0" use="optional">
<xsd:annotation>
<xsd:documentation>
Gives the Z position of the image plane at the specified IFD. Indexed from 0.
Default is 0 (the first Z position). [units:none]
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="FirstT" type="NonNegativeInt" default="0" use="optional">
<xsd:annotation>
<xsd:documentation>
Gives the T position of the image plane at the specified IFD. Indexed from 0.
Default is 0 (the first T position). [units:none]
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="FirstC" type="NonNegativeInt" default="0" use="optional">
<xsd:annotation>
<xsd:documentation>
Gives the C position of the image plane at the specified IFD. Indexed from 0.
Default is 0 (the first C position). [units:none]
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="PlaneCount" use="optional" type="NonNegativeInt">
<xsd:annotation>
<xsd:documentation>
Gives the number of IFDs affected. Dimension order of IFDs is given by the enclosing
Pixels element's DimensionOrder attribute. Default is the number of IFDs in the TIFF
file, unless an IFD is specified, in which case the default is 1. [units:none]
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<xsd:element name="StageLabel"> <!-- top level definition -->
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><plural>StageLabels</plural></xsdfu></xsd:appinfo>
<xsd:documentation>
The StageLabel is used to specify a name and position for a stage position in the microscope's reference frame.
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:attribute name="Name" use="required" type="xsd:string"/>
<xsd:attribute name="X" use="optional" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
The X position of the stage label. Units are set by XUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="XUnit" use="optional" default="reference frame" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the X stage position - default:[reference frame].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="Y" use="optional" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
The Y position of the stage label. Units are set by YUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="YUnit" use="optional" default="reference frame" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the Y stage position - default:[reference frame].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="Z" use="optional" type="xsd:float">
<xsd:annotation>
<xsd:documentation>
The Z position of the stage label. Units are set by ZUnit.
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="ZUnit" use="optional" default="reference frame" type="UnitsLength">
<xsd:annotation>
<xsd:documentation>The units of the Z stage position - default:[reference frame].</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<!-- Misc -->
<xsd:element name="MicrobeamManipulation"> <!-- top level definition -->
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><plural>MicrobeamManipulations</plural></xsdfu></xsd:appinfo>
<xsd:documentation>
Defines a microbeam operation type and the region of the image it was applied to.
The LightSourceRef element is a reference to a LightSource specified in the Instrument element which was used for a technique other than illumination for
the purpose of imaging. For example, a laser used for photobleaching.
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element name="Description" minOccurs="0" maxOccurs="1">
<xsd:annotation>
<xsd:documentation>
A description for the Microbeam Manipulation. [plain-text multi-line string]
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:whiteSpace value="preserve"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:element>
<xsd:element ref="ROIRef" minOccurs="1" maxOccurs="unbounded">
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><manytomany/></xsdfu></xsd:appinfo>
</xsd:annotation>
</xsd:element>
<xsd:element ref="ExperimenterRef" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="LightSourceSettings" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="ID" use="required" type="MicrobeamManipulationID"/>
<xsd:attribute name="Type" use="optional">
<xsd:annotation>
<xsd:documentation>
The type of manipulation performed.
</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:list>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="FRAP"/><!-- Fluorescence recovery after photobleaching -->
<xsd:enumeration value="FLIP"/><!-- Fluorescence Loss in Photobleaching -->
<xsd:enumeration value="InverseFRAP"/><!-- iFRAP, inverse FRAP -->
<xsd:enumeration value="Photoablation"/>
<xsd:enumeration value="Photoactivation"/>
<xsd:enumeration value="Uncaging"/>
<xsd:enumeration value="OpticalTrapping"/>
<xsd:enumeration value="Other"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:list>
</xsd:simpleType>
</xsd:attribute>
</xsd:complexType>
</xsd:element>
<!-- Physical microscope elements -->
<xsd:element name="Instrument"> <!-- top level definition -->
<xsd:annotation>
<xsd:appinfo><xsdfu xmlns=""><plural>Instruments</plural></xsdfu></xsd:appinfo>
<xsd:documentation>
This element describes the instrument used to capture the Image.
It is primarily a container for manufacturer's model and catalog
numbers for the Microscope, LightSource, Detector, Objective and
Filters components.
The Objective element contains the additional elements LensNA and Magnification.
The Filters element can be composed either of separate excitation,
emission filters and a dichroic mirror or a single filter set.
Within the Image itself, a reference is made to this one Filter element.
There may be multiple light sources, detectors, objectives and filters on a microscope.
Each of these has their own ID attribute, which can be referred to from Channel.
It is understood that the light path configuration can be different
for each channel, but cannot be different for each timepoint or
each plane of an XYZ stack.
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="Microscope" minOccurs="0" maxOccurs="1"/>