source: trunk/components/bio-formats-auto/src/entities.txt @ 4671

Revision 4671, 32.2 KB checked in by melissa, 12 years ago (diff)

Added the Iris property of Objective to the MetadataStore and MetadataRetrieve interfaces. Note that this property is not supported by existing OME-XML schemas, but will be present in the next release. It is being added now to support OMERO's needs.

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1#
2# entities.txt
3#
4
5# OME Bio-Formats package for reading and converting biological file formats.
6# Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
7#
8# This program is free software; you can redistribute it and/or modify
9# it under the terms of the GNU General Public License as published by
10# the Free Software Foundation; either version 3 of the License, or
11# (at your option) any later version.
12#
13# This program is distributed in the hope that it will be useful,
14# but WITHOUT ANY WARRANTY; without even the implied warranty of
15# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
16# GNU General Public License for more details.
17#
18# You should have received a copy of the GNU General Public License
19# along with this program; if not, write to the Free Software
20# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
21
22# This file enumerates the metadata entity and property definitions for the
23# loci.formats.meta package, and loci.formats.ome.OMEXML*Metadata classes.
24
25# Path elements ending in plus (+) have maxOccurs > 1 and generate an
26# index parameter to allow differentiation between them.
27
28### Entities for 5D Image information ###
29
30## Image ##
31
32[Image]
33countable = true
34path = Image+
35description = an image in the metadata store
36
37[Image ID]
38type = String
39getter = getNodeID
40setter = setNodeID
41description = unique label identifying the image
42
43[Image Name]
44type = String
45description = the full name of the image
46
47[Image CreationDate]
48type = String
49description = the creation date of the image
50
51[Image Description]
52type = String
53description = the full description of the image
54
55[Image InstrumentRef]
56type = String
57description = label reference for the associated instrument
58
59[Image DefaultPixels]
60type = String
61description = default pixels set for the image
62
63## Pixels ##
64
65[Pixels]
66countable = true
67path = Image+/Pixels+
68description = a pixels set in the metadata store
69
70[Pixels ID]
71type = String
72getter = getNodeID
73setter = setNodeID
74description = unique label identifying the pixels set
75
76[Pixels SizeX]
77type = Integer
78description = The size of an individual plane or section's X axis (width).
79
80[Pixels SizeY]
81type = Integer
82description = The size of an individual plane or section's Y axis (height).
83
84[Pixels SizeZ]
85type = Integer
86description = number of optical sections per stack
87
88[Pixels SizeC]
89type = Integer
90description = number of channels per timepoint
91
92[Pixels SizeT]
93type = Integer
94description = number of timepoints
95
96[Pixels PixelType]
97type = String
98description = the pixel type
99
100[Pixels BigEndian]
101type = Boolean
102description = endianness of the pixels set
103
104[Pixels DimensionOrder]
105type = String
106description = the dimension order of the pixels set
107
108## TiffData ##
109
110[TiffData]
111countable = true
112path = Image+/Pixels+/TiffData+
113description = TODO
114
115[TiffData FirstZ]
116type = Integer
117description = TODO
118
119[TiffData FirstT]
120type = Integer
121description = TODO
122
123[TiffData FirstC]
124type = Integer
125description = TODO
126
127[TiffData IFD]
128type = Integer
129description = TODO
130
131[TiffData NumPlanes]
132type = Integer
133description = TODO
134
135[TiffData UUID]
136path = Image+/Pixels+/TiffData+/UUID
137type = String
138getter = getCData
139setter = setCData
140description = TODO
141
142[TiffData UUID 200706]
143path = -
144
145[TiffData UUID 2003FC]
146path = -
147
148[TiffData FileName]
149path = Image+/Pixels+/TiffData+/UUID
150type = String
151description = TODO
152
153[TiffData FileName 200706]
154path = -
155
156[TiffData FileName 2003FC]
157path = -
158
159## Dimensions ##
160
161[Dimensions]
162path = Image+/Pixels+
163description = a set of pixel dimensions in the metadata store \
164              with a particular index
165
166[Dimensions 2003FC]
167path = Image+
168
169[Dimensions PhysicalSizeX]
170type = Float
171description = the size of an individual pixel's X axis in microns
172
173[Dimensions PhysicalSizeX 2003FC]
174getter = getPixelSizeX
175setter = setPixelSizeX
176
177[Dimensions PhysicalSizeY]
178type = Float
179description = the size of an individual pixel's Y axis in microns
180
181[Dimensions PhysicalSizeY 2003FC]
182getter = getPixelSizeY
183setter = setPixelSizeY
184
185[Dimensions PhysicalSizeZ]
186type = Float
187description = the size of an individual pixel's Z axis in microns
188
189[Dimensions PhysicalSizeZ 2003FC]
190getter = getPixelSizeZ
191setter = setPixelSizeZ
192
193[Dimensions TimeIncrement]
194type = Float
195description = the distance between adjacent time points in seconds
196
197[Dimensions WaveStart]
198type = Integer
199description = the starting wavelength in nanometers
200
201[Dimensions WaveIncrement]
202type = Integer
203description = the distance between adjacent wavelengths in nanometers
204
205## ImagingEnvironment ##
206
207[ImagingEnvironment]
208path = Image+/ImagingEnvironment
209description = the imaging environment for a particular image
210
211[ImagingEnvironment Temperature]
212type = Float
213description = TODO
214
215[ImagingEnvironment AirPressure]
216type = Float
217description = TODO
218
219[ImagingEnvironment Humidity]
220type = Float
221description = TODO
222
223[ImagingEnvironment CO2Percent]
224type = Float
225description = TODO
226
227## Plane ##
228
229[Plane]
230countable = true
231path = Image+/Pixels+/Plane+
232description = the plane information for a specific X-Y plane (section) \
233              within a particular pixels set
234
235[Plane 2003FC]
236path = -
237
238[Plane TheZ]
239type = Integer
240description = the optical section index
241
242[Plane TheC]
243type = Integer
244description = the channel index
245
246[Plane TheT]
247type = Integer
248description = the timepoint
249
250## PlaneTiming ##
251
252[PlaneTiming]
253path = Image+/Pixels+/Plane+/PlaneTiming
254description = the timing information for a specific X-Y plane (section) \
255              within a particular pixels set
256
257[PlaneTiming 2003FC]
258path = -
259
260[PlaneTiming DeltaT]
261type = Float
262description = the time in seconds since the beginning of the experiment
263
264[PlaneTiming ExposureTime]
265type = Float
266description = the exposure time in seconds
267
268## StagePosition ##
269
270[StagePosition]
271path = Image+/Pixels+/Plane+/StagePosition
272description = the stage position for a specific X-Y plane (section) \
273              within a particular pixels set
274
275[StagePosition 2003FC]
276path = -
277
278[StagePosition PositionX]
279type = Float
280description = the X coordinate of the stage position
281
282[StagePosition PositionY]
283type = Float
284description = the Y coordinate of the stage position
285
286[StagePosition PositionZ]
287type = Float
288description = the Z coordinate of the stage position
289
290### Entities for channel information for a particular Image ###
291
292## LogicalChannel ##
293
294[LogicalChannel]
295countable = true
296path = Image+/LogicalChannel+
297description = a logical channel and physical channel in the metadata store \
298              for a particular pixels set
299
300[LogicalChannel 2003FC]
301path = Image+/ChannelInfo+
302
303[LogicalChannel ID]
304type = String
305getter = getNodeID
306setter = setNodeID
307description = unique label identifying the logical channel
308
309[LogicalChannel Name]
310type = String
311description = the logical channel's name
312
313[LogicalChannel SamplesPerPixel]
314type = Integer
315description = TODO
316
317[LogicalChannel IlluminationType]
318type = String
319description = the illumination type
320
321[LogicalChannel PinholeSize]
322type = Float
323description = the size of the pinhole
324
325[LogicalChannel PinholeSize 200802]
326type = Integer
327
328[LogicalChannel PinholeSize 200706]
329type = Integer
330
331[LogicalChannel PinholeSize 2003FC]
332type = Integer
333
334[LogicalChannel PhotometricInterpretation]
335type = String
336description = the photometric interpretation type
337
338[LogicalChannel Mode]
339type = String
340description = the acquisition mode
341
342[LogicalChannel ContrastMethod]
343type = String
344description = the constrast method name
345
346[LogicalChannel ExWave]
347type = Integer
348description = the excitation wavelength
349
350[LogicalChannel EmWave]
351type = Integer
352description = the emission wavelength
353
354[LogicalChannel Fluor]
355type = String
356description = the fluorescence type
357
358[LogicalChannel NdFilter]
359type = Float
360description = the neutral-density filter value
361
362[LogicalChannel NdFilter 2003FC]
363getter = getNDfilter
364setter = setNDfilter
365
366[LogicalChannel PockelCellSetting]
367type = Integer
368description = TODO
369
370[LogicalChannel PockelCellSetting 2003FC]
371path = -
372
373[LogicalChannel OTF]
374path = Image+/LogicalChannel+/OTFRef
375type = String
376getter = getNodeID
377setter = setNodeID
378description = the OTF associated with the logical channel
379
380[LogicalChannel OTF 2003FC]
381path = Image+/ChannelInfo+/OTFRef
382
383## ChannelComponent ##
384
385[ChannelComponent]
386countable = true
387path = Image+/LogicalChannel+/ChannelComponent+
388description = a channel component describes how each channel \
389              in the pixel array relates to the logical channels
390
391[ChannelComponent 2003FC]
392path = Image+/ChannelInfo+/ChannelComponent+
393
394[ChannelComponent Index]
395type = Integer
396description = the index into the channel dimension of the 5-D pixel array
397
398[ChannelComponent ColorDomain]
399type = String
400description = which color channel this ChannelComponent belongs to \
401              (for example, 'R' for an 'RGB' PhotometricInterpretation)
402
403# FIXME xsd-fu needs to include get/setPixels methods in ChannelComponentNode?
404#[ChannelComponent Pixels]
405#type = String
406#description = the pixels to which this channel component corresponds
407
408## DisplayOptions ##
409
410[DisplayOptions]
411path = Image+/DisplayOptions
412description = various display options for a particular pixels set
413
414[DisplayOptions ID]
415type = String
416getter = getNodeID
417setter = setNodeID
418description = unique label identifying the display options
419
420# FIXME xsd-fu needs to include get/setPixels methods in DisplayOptionsNode
421#[DisplayOptions Pixels]
422#type = String
423#description = the pixels to which these display options correspond
424
425[DisplayOptions Zoom]
426type = Float
427description = zoom factor for use in the display (NOT THE LENS ZOOM)
428
429## RedChannel ##
430
431# FIXME xsd-fu needs to include RedChannelNode (extension of ChannelSpecNode)
432#[RedChannel]
433#path = Image+/DisplayOptions/RedChannel
434#description = information about the red channel for a particular image
435#
436# FIXME the 2003FC path below will cause compilation errors because RedChannel
437# is not of type RedChannelNode, but DisplayChannelNode; need a notation to
438# specify the distinction between node type and method getter name
439#[RedChannel 2003FC]
440#path = Image+/CA/DisplayOptions/RedChannel
441#
442#[RedChannel ChannelNumber]
443#type = Integer
444#description = TODO
445#
446#[RedChannel WhiteLevel]
447#type = Float
448#description = TODO
449#
450#[RedChannel BlackLevel]
451#type = Float
452#description = TODO
453#
454#[RedChannel Gamma]
455#type = Float
456#description = TODO
457
458## RedChannelToggle ##
459
460# FIXME xsd-fu needs to include RedChannelNode (extension of ChannelSpecNode)
461#[RedChannelToggle]
462#description = visibility toggle for a particular image's red channel
463#path = Image+/DisplayOptions/RedChannel
464#
465#[RedChannelToggle 2003FC]
466#path = Image+/CA/DisplayOptions
467#
468#[RedChannelToggle Enabled]
469#type = Boolean
470#getter = getisOn
471#setter = setisOn
472#description = indicator for whether red channel is active in the display
473#
474#[RedChannelToggle Enabled 2003FC
475#getter = isRedChannelOn
476#setter = setRedChannelOn
477
478## GreenChannel ##
479
480# FIXME xsd-fu needs to include GreenChannelNode (extension of ChannelSpecNode)
481#[GreenChannel]
482#path = Image+/DisplayOptions/GreenChannel
483#description = information about the green channel for a particular image
484#
485# FIXME the 2003FC path below will cause compilation errors because GreenChannel
486# is not of type GreenChannelNode, but DisplayChannelNode; need a notation to
487# specify the distinction between node type and method getter name
488#[GreenChannel 2003FC]
489#path = Image+/CA/DisplayOptions/GreenChannel
490#
491#[GreenChannel ChannelNumber]
492#type = Integer
493#description = TODO
494#
495#[GreenChannel WhiteLevel]
496#type = Float
497#description = TODO
498#
499#[GreenChannel BlackLevel]
500#type = Float
501#description = TODO
502#
503#[GreenChannel Gamma]
504#type = Float
505#description = TODO
506
507## GreenChannelToggle ##
508
509# FIXME xsd-fu needs to include GreenChannelNode (extension of ChannelSpecNode)
510#[GreenChannelToggle]
511#description = visibility toggle for a particular image's green channel
512#path = Image+/DisplayOptions/GreenChannel
513#
514#[GreenChannelToggle 2003FC]
515#path = Image+/CA/DisplayOptions
516#
517#[GreenChannelToggle Enabled]
518#type = Boolean
519#getter = getisOn
520#setter = setisOn
521#description = indicator for whether Green channel is active in the display
522#
523#[GreenChannelToggle Enabled 2003FC
524#getter = isGreenChannelOn
525#setter = setGreenChannelOn
526
527## BlueChannel ##
528
529# FIXME xsd-fu needs to include BlueChannelNode (extension of ChannelSpecNode)
530#[BlueChannel]
531#path = Image+/DisplayOptions/BlueChannel
532#description = information about the blue channel for a particular image
533#
534# FIXME the 2003FC path below will cause compilation errors because BlueChannel
535# is not of type BlueChannelNode, but DisplayChannelNode; need a notation to
536# specify the distinction between node type and method getter name
537#[BlueChannel 2003FC]
538#path = Image+/CA/DisplayOptions/BlueChannel
539#
540#[BlueChannel ChannelNumber]
541#type = Integer
542#description = TODO
543#
544#[BlueChannel WhiteLevel]
545#type = Float
546#description = TODO
547#
548#[BlueChannel BlackLevel]
549#type = Float
550#description = TODO
551#
552#[BlueChannel Gamma]
553#type = Float
554#description = TODO
555
556## BlueChannelToggle ##
557
558# FIXME xsd-fu needs to include BlueChannelNode (extension of ChannelSpecNode)
559#[BlueChannelToggle]
560#description = visibility toggle for a particular image's blue channel
561#path = Image+/DisplayOptions/BlueChannel
562#
563#[BlueChannelToggle 2003FC]
564#path = Image+/CA/DisplayOptions
565#
566#[BlueChannelToggle Enabled]
567#type = Boolean
568#getter = getisOn
569#setter = setisOn
570#description = indicator for whether red channel is active in the display
571#
572#[BlueChannelToggle Enabled 2003FC
573#getter = isBlueChannelOn
574#setter = setBlueChannelOn
575
576## GreyChannel ##
577
578# FIXME xsd-fu needs to include GreyChannelNode
579#[GreyChannel]
580#path = Image+/DisplayOptions/GreyChannel
581#description = information about the grey channel for a particular image
582#
583# FIXME the 2003FC path below will cause compilation errors because
584# GreyChannel is not of type GreyChannelNode, but DisplayChannelNode; need a
585# notation to specify the distinction between node type and method getter name
586#[GreyChannel 2003FC]
587#path = Image+/CA/DisplayOptions/GreyChannel
588#
589#[GreyChannel ChannelNumber]
590#type = Integer
591#description = TODO
592#
593#[GreyChannel WhiteLevel]
594#type = Float
595#description = TODO
596#
597#[GreyChannel BlackLevel]
598#type = Float
599#description = TODO
600#
601#[GreyChannel Gamma]
602#type = Float
603#description = TODO
604
605## GreyChannelMap ##
606
607# FIXME xsd-fu needs to include GreyChannelNode
608#[GreyChannelMap]
609#path = Image+/DisplayOptions/GreyChannel
610#description = color map setting for a particular image's grey channel
611#
612#[GreyChannelMap 2003FC]
613#path = Image+/CA/DisplayOptions
614#
615#[GreyChannelMap ColorMap]
616#type = String
617#description = TODO
618#
619# FIXME need to implement this conversion method in OMEXMLNode
620#[GreyChannelMap ColorMap 2003FC]
621#type = Boolean
622#getter = isDisplayRGB
623#setter = setDisplayRGB
624
625## DisplayOptionsProjection ##
626
627[DisplayOptionsProjection]
628path = Image+/DisplayOptions/Projection
629description = maximum intensity projection-related display options \
630              for a particular image
631
632[DisplayOptionsProjection ZStart]
633type = Integer
634description = the first focal plane to include \
635              in the maximum intensity projection
636
637[DisplayOptionsProjection ZStart 2003FC]
638getter = getZstart
639setter = setZstart
640
641[DisplayOptionsProjection ZStop]
642type = Integer
643description = the last focal plane to include \
644              in the maximum intensity projection
645
646[DisplayOptionsProjection ZStop 2003FC]
647getter = getZstop
648setter = setZstop
649
650## DisplayOptionsTime ##
651
652[DisplayOptionsTime]
653path = Image+/DisplayOptions/Time
654description = time range-related display options for a particular image
655
656[DisplayOptionsTime TStart]
657type = Integer
658description = the first time point to include in the animation
659
660[DisplayOptionsTime TStart 2003FC]
661getter = getTstart
662setter = setTstart
663
664[DisplayOptionsTime TStop]
665type = Integer
666description = the last time point to include in the animation
667
668[DisplayOptionsTime TStop 2003FC]
669getter = getTstop
670setter = setTstop
671
672## ROI ##
673
674[ROI]
675countable = true
676path = Image+/DisplayOptions/ROI+
677description = a 5D bounding box region of interest in the metadata store \
678              with a particular index
679
680[ROI 200809]
681path = -
682
683[ROI ID]
684type = String
685getter = getNodeID
686setter = setNodeID
687description = unique label identifying the 5D bounding box ROI
688
689[ROI X0]
690type = Integer
691description = the starting X coordinate
692
693[ROI Y0]
694type = Integer
695description = the starting Y coordinate
696
697[ROI X1]
698type = Integer
699description = the ending X coordinate
700
701[ROI Y1]
702type = Integer
703description = the ending Y coordinate
704
705[ROI Z0]
706type = Integer
707description = the starting Z coordinate
708
709[ROI Z1]
710type = Integer
711description = the ending Z coordinate
712
713[ROI T0]
714type = Integer
715description = the starting timepoint
716
717[ROI T1]
718type = Integer
719description = the ending timepoint
720
721### Entities for Instrument settings for a particular Image ###
722
723## ObjectiveSettings ##
724
725[ObjectiveSettings]
726path = Image+/ObjectiveRef
727description = the objective associated with a particular image
728
729[ObjectiveSettings 200706]
730path = Image+/ObjectiveSettings
731description = TODO
732
733[ObjectiveSettings Objective]
734type = String
735getter = getNodeID
736setter = setNodeID
737description = the objective associated with this image
738
739[ObjectiveSettings RefractiveIndex]
740type = Float
741description = unit-less refractive index of the immersion medium
742
743[ObjectiveSettings RefractiveIndex 2003FC]
744path = -
745
746[ObjectiveSettings CorrectionCollar]
747type = Float
748description = unit-less setting of the adjustable correction collar
749
750[ObjectiveSettings CorrectionCollar 2003FC]
751path = -
752
753[ObjectiveSettings Medium]
754type = String
755description = immersion medium for the lens
756
757[ObjectiveSettings Medium 2003FC]
758path = -
759
760## DetectorSettings ##
761
762[DetectorSettings]
763path = Image+/LogicalChannel+/DetectorRef
764description = the detector associated with a particular logical channel
765
766[DetectorSettings 2003FC]
767path = Image+/ChannelInfo+/DetectorRef
768
769[DetectorSettings Detector]
770type = String
771getter = getNodeID
772setter = setNodeID
773description = the detector associated with this channel
774
775[DetectorSettings Offset]
776type = Float
777description = the detector offset
778
779[DetectorSettings Gain]
780type = Float
781description = the detector gain
782
783[DetectorSettings Binning]
784type = String
785description = the detector binning
786
787[DetectorSettings Binning 2003FC]
788path = -
789
790[DetectorSettings Voltage]
791type = Float
792description = TODO
793
794[DetectorSettings Voltage 2003FC]
795path = -
796
797[DetectorSettings ReadOutRate]
798type = Float
799description = TODO
800
801[DetectorSettings ReadOutRate 2003FC]
802path = -
803
804## LightSourceSettings ##
805
806[LightSourceSettings]
807path = Image+/LogicalChannel+/LightSourceRef
808description = the light source associated with a particular logical channel
809
810[LightSourceSettings 2003FC]
811path = Image+/ChannelInfo+/LightSourceRef
812
813[LightSourceSettings LightSource]
814type = String
815getter = getNodeID
816setter = setNodeID
817description = the primary light source
818
819[LightSourceSettings Attenuation]
820type = Float
821description = the primary light source attenuation
822
823[LightSourceSettings Wavelength]
824type = Integer
825description = the primary light source wavelength
826
827### Entities for other Image-specific information ###
828
829## StageLabel ##
830
831[StageLabel]
832path = Image+/StageLabel
833description = a stage label in the metadata store with a particular index
834
835[StageLabel Name]
836type = String
837description = a name for the stage label
838
839[StageLabel X]
840type = Float
841description = the x coordinate of the stage
842
843[StageLabel Y]
844type = Float
845description = the y coordinate of the stage
846
847[StageLabel Z]
848type = Float
849description = the z coordinate of the stage
850
851### Entities for Instrument hardware -- these DO NOT vary by Image ###
852
853## Instrument ##
854
855[Instrument]
856countable = true
857path = Instrument+
858description = information about a microscope or other instrument
859
860[Instrument ID]
861type = String
862getter = getNodeID
863setter = setNodeID
864description = unique label identifying the instrument
865
866## LightSource ##
867
868[LightSource]
869countable = true
870path = Instrument+/LightSource+
871description = a light source for a particular instrument
872
873[LightSource ID]
874type = String
875getter = getNodeID
876setter = setNodeID
877description = unique label identifying the light source
878
879[LightSource Manufacturer]
880type = String
881description = TODO
882
883[LightSource Model]
884type = String
885description = TODO
886
887[LightSource SerialNumber]
888type = String
889description = TODO
890
891[LightSource Power]
892type = Float
893description = TODO
894
895[LightSource Power 200706]
896path = -
897
898[LightSource Power 2003FC]
899path = -
900
901## Laser ##
902
903[Laser]
904path = Instrument+/LightSource+/Laser
905description = a laser for a particular instrument
906
907[Laser Type]
908type = String
909description = TODO
910
911[Laser LaserMedium]
912type = String
913description = TODO
914
915[Laser LaserMedium 2003FC]
916getter = getMedium
917setter = setMedium
918
919[Laser Wavelength]
920type = Integer
921description = TODO
922
923[Laser FrequencyMultiplication]
924type = Integer
925description = TODO
926
927[Laser FrequencyMultiplication 2003FC]
928type = Boolean
929getter = getFrequencyDoubled
930setter = setFrequencyDoubled
931
932[Laser Tuneable]
933type = Boolean
934description = TODO
935
936[Laser Tuneable 2003FC]
937getter = getTunable
938setter = setTunable
939
940[Laser Pulse]
941type = String
942description = TODO
943
944## Filament ##
945
946[Filament]
947path = Instrument+/LightSource+/Filament
948description = a filament for a particular instrument
949
950[Filament Type]
951type = String
952description = TODO
953
954## Arc ##
955
956[Arc]
957path = Instrument+/LightSource+/Arc
958description = an arc for a particular instrument
959
960[Arc Type]
961type = String
962description = TODO
963
964## Detector ##
965
966[Detector]
967countable = true
968path = Instrument+/Detector+
969description = a detector for a particular instrument
970
971[Detector ID]
972type = String
973getter = getNodeID
974setter = setNodeID
975description = unique label identifying the detector
976
977[Detector Manufacturer]
978type = String
979description = TODO
980
981[Detector Model]
982type = String
983description = TODO
984
985[Detector SerialNumber]
986type = String
987description = TODO
988
989[Detector Type]
990type = String
991description = TODO
992
993[Detector Gain]
994type = Float
995description = TODO
996
997[Detector Voltage]
998type = Float
999description = TODO
1000
1001[Detector Offset]
1002type = Float
1003description = TODO
1004
1005## Objective ##
1006
1007[Objective]
1008countable = true
1009path = Instrument+/Objective+
1010description = an objective for a particular instrument
1011
1012[Objective ID]
1013type = String
1014getter = getNodeID
1015setter = setNodeID
1016description = unique label identifying the objective
1017
1018[Objective Manufacturer]
1019type = String
1020description = TODO
1021
1022[Objective Model]
1023type = String
1024description = TODO
1025
1026[Objective SerialNumber]
1027type = String
1028description = TODO
1029
1030[Objective Correction]
1031type = String
1032description = TODO
1033
1034[Objective Correction 2003FC]
1035path = -
1036
1037[Objective Immersion]
1038type = String
1039description = TODO
1040
1041[Objective Immersion 2003FC]
1042path = -
1043
1044[Objective LensNA]
1045type = Float
1046description = TODO
1047
1048[Objective NominalMagnification]
1049type = Integer
1050description = TODO
1051
1052[Objective NominalMagnification 2003FC]
1053path = -
1054
1055[Objective CalibratedMagnification]
1056type = Float
1057description = TODO
1058
1059[Objective CalibratedMagnification 2003FC]
1060getter = getMagnification
1061setter = setMagnification
1062
1063[Objective WorkingDistance]
1064type = Float
1065description = TODO
1066
1067[Objective WorkingDistance 2003FC]
1068path = -
1069
1070# NB: This will be added in the next OME-XML release.
1071[Objective Iris]
1072type = Boolean
1073description = TODO
1074
1075[Objective Iris 200809]
1076path = -
1077
1078[Objective Iris 200802]
1079path = -
1080
1081[Objective Iris 200706]
1082path = -
1083
1084[Objective Iris 2003FC]
1085path = -
1086
1087#TODO figure out how to reconcile the two filter models
1088
1089#http://www.openmicroscopy.org/Schemas/OME/2007-06/ome.xsd
1090#http://ome-xml.org/wiki/FilterAndFilterSet
1091
1092#http://www.openmicroscopy.org/XMLschemas/OME/FC/ome.xsd
1093#http://openmicroscopy.org/api/xml/OME/ome-instrument.html
1094
1095## ExcitationFilter ##
1096
1097#[ExcitationFilter]
1098#path = ?
1099#description = an excitation filter for a particular instrument
1100#
1101#[ExcitationFilter 2003FC]
1102#path = CA/ExcitationFilter+
1103#
1104#[ExcitationFilter Manufacturer]
1105#type = String
1106#description = TODO
1107#
1108#[ExcitationFilter Model]
1109#type = String
1110#description = TODO
1111#
1112#[ExcitationFilter LotNumber]
1113#type = String
1114#description = TODO
1115#
1116#[ExcitationFilter Type]
1117#type = String
1118#description = TODO
1119
1120## Dichroic ##
1121
1122#[Dichroic]
1123#path = ?
1124#description = a dichroic for a particular instrument
1125#
1126#[Dichroic 2003FC]
1127#path = CA/Dichroic+
1128#
1129#[Dichroic Manufacturer]
1130#type = String
1131#description = TODO
1132#
1133#[Dichroic Model]
1134#type = String
1135#description = TODO
1136#
1137#[Dichroic LotNumber]
1138#type = String
1139#description = TODO
1140
1141## EmissionFilter ##
1142
1143#[EmissionFilter]
1144#path = ?
1145#description = an emission filter for a particular instrument
1146#
1147#[EmissionFilter 2003FC]
1148#path = CA/EmissionFilter+
1149#
1150#[EmissionFilter Manufacturer]
1151#type = String
1152#description = TODO
1153#
1154#[EmissionFilter Model]
1155#type = String
1156#description = TODO
1157#
1158#[EmissionFilter LotNumber]
1159#type = String
1160#description = TODO
1161#
1162#[EmissionFilter Type]
1163#type = String
1164#description = TODO
1165
1166## FilterSet ##
1167
1168#[FilterSet]
1169#path = ?
1170#description = a filter set for a particular instrument
1171#
1172#[FilterSet 2003FC]
1173#path = CA/FilterSet+
1174#
1175#[FilterSet Manufacturer]
1176#type = String
1177#description = TODO
1178#
1179#[FilterSet Model]
1180#type = String
1181#description = TODO
1182#
1183#[FilterSet LotNumber]
1184#type = String
1185#description = TODO
1186
1187## OTF ##
1188
1189[OTF]
1190countable = true
1191path = Instrument+/OTF+
1192description = an optical transfer function for a particular instrument
1193
1194[OTF ID]
1195type = String
1196getter = getNodeID
1197setter = setNodeID
1198description = unique label identifying the optical transfer function
1199
1200[OTF SizeX]
1201type = Integer
1202description = TODO
1203
1204[OTF SizeY]
1205type = Integer
1206description = TODO
1207
1208[OTF PixelType]
1209type = String
1210description = TODO
1211
1212[OTF OpticalAxisAveraged]
1213type = Boolean
1214description = TODO
1215
1216[OTF OpticalAxisAveraged 2003FC]
1217getter = getOpticalAxisAvrg
1218setter = setOpticalAxisAvrg
1219
1220[OTF Objective]
1221path = Instrument+/OTF+/ObjectiveRef
1222type = String
1223getter = getNodeID
1224setter = setNodeID
1225description = objective described by the optical transfer function
1226
1227### Entities for Experiment & Experimenter details ###
1228
1229## Experiment ##
1230
1231[Experiment]
1232countable = true
1233path = Experiment+
1234description = information about a particular experiment
1235
1236[Experiment ID]
1237type = String
1238getter = getNodeID
1239setter = setNodeID
1240description = unique label identifying the experiment
1241
1242[Experiment Description]
1243type = String
1244description = TODO
1245
1246[Experiment Type]
1247type = String
1248description = TODO
1249
1250#[Experiment Experimenter]
1251#TODO - need Experiment.setExperimenter in OME-XML Java library
1252
1253## Experimenter ##
1254
1255[Experimenter]
1256countable = true
1257path = Experimenter+
1258description = information about someone performing an experiment
1259
1260[Experimenter ID]
1261type = String
1262getter = getNodeID
1263setter = setNodeID
1264description = unique label identifying the experimenter
1265
1266[Experimenter FirstName]
1267type = String
1268description = the first name of the experimenter
1269
1270[Experimenter LastName]
1271type = String
1272description = the last name of the experimenter
1273
1274[Experimenter Email]
1275type = String
1276description = the e-mail address of the experimenter
1277
1278[Experimenter Institution]
1279type = String
1280description = the institution to which the experimenter belongs
1281
1282## GroupRef ##
1283
1284[GroupRef]
1285countable = true
1286path = Experimenter+/GroupRef+
1287description = HACK - force creation of MetadataRetrieve.getGroupRefCount(int)
1288
1289## ExperimenterMembership ##
1290
1291[ExperimenterMembership]
1292countable = true
1293path = Experimenter+/GroupRef+
1294description = a linkage between a particular experimenter and a group
1295
1296[ExperimenterMembership Group]
1297type = String
1298getter = getNodeID
1299setter = setNodeID
1300description = the group associated with this membership
1301
1302### Entities for high-content screening ###
1303
1304## Plate ##
1305
1306[Plate]
1307countable = true
1308path = Plate+
1309description = identifies a plate within a screen
1310
1311[Plate 2003FC]
1312path = -
1313
1314[Plate ID]
1315type = String
1316getter = getNodeID
1317setter = setNodeID
1318description = unique label identifying the plate
1319
1320#[Plate ScreenRef]
1321#type =
1322#description = TODO
1323
1324[Plate Name]
1325type = String
1326description = the plate's name
1327
1328[Plate Description]
1329type = String
1330
1331[Plate Status]
1332type = String
1333description = current state of the plate with respect to the experiment work-flow
1334
1335[Plate ExternalIdentifier]
1336type = String
1337description = reference to this plate in an external database
1338
1339## PlateRef ##
1340
1341[PlateRef]
1342countable = true
1343path = Screen+/PlateRef+
1344description = reference to a Plate element
1345
1346[PlateRef 2003FC]
1347path = -
1348
1349[PlateRef ID]
1350type = String
1351getter = getNodeID
1352setter = setNodeID
1353description = label reference for the associated plate
1354
1355## Reagent ##
1356
1357[Reagent]
1358countable = true
1359path = Screen+/Reagent+
1360description = describes a chemical or other physical experimental parameter
1361
1362[Reagent 2003FC]
1363path = -
1364
1365[Reagent ID]
1366type = String
1367getter = getNodeID
1368setter = setNodeID
1369description = unique label identifying the reagent
1370
1371[Reagent Description]
1372type = String
1373description = the reagent's description
1374
1375[Reagent Name]
1376type = String
1377description = the reagent's name
1378
1379[Reagent ReagentIdentifier]
1380type = String
1381description = reference to this reagent in an external database
1382
1383## ReagentRef ##
1384
1385#[ReagentRef]
1386#countable = true
1387#path = Screen+/ReagentRef+
1388#description = reference to a Reagent
1389
1390#[ReagentRef 2003FC]
1391#path = -
1392
1393#[ReagentRef ID]
1394#type = String
1395#getter = getNodeID
1396#setter = setNodeID
1397#description = label reference for the associated reagent
1398
1399## Screen ##
1400
1401[Screen]
1402countable = true
1403path = Screen+
1404description = description of a screen (grouping of plates)
1405
1406[Screen 2003FC]
1407path = -
1408
1409#[Screen PlateRef]
1410#type = String
1411#description = label reference for the associated plate
1412
1413[Screen ID]
1414type = String
1415getter = getNodeID
1416setter = setNodeID
1417description = unique label identifying the screen
1418
1419[Screen Name]
1420type = String
1421description = the screen's name
1422
1423[Screen ProtocolIdentifier]
1424type = String
1425description = reference to an externally defined protocol
1426
1427[Screen ProtocolDescription]
1428type = String
1429description = description of the screen's protocol
1430
1431[Screen ReagentSetDescription]
1432type = String
1433description = description of a set of reagents
1434
1435#[Screen ReagentSetidentifier]
1436#type = String
1437#description = reference to an externally defined set of reagents
1438
1439[Screen Type]
1440type = String
1441description = human-readable screen type, e.g. RNAi, cDNA
1442
1443## ScreenRef ##
1444
1445#[ScreenRef]
1446#countable = true
1447#path = Screen+/ScreenRef+
1448#description = reference to a Screen element
1449
1450#[ScreenRef 2003FC]
1451#path = -
1452
1453#[ScreenRef ID]
1454#type = String
1455#getter = getNodeID
1456#setter = setNodeID
1457#description = label reference for the associated screen
1458
1459## ScreenAcquisition ##
1460
1461[ScreenAcquisition]
1462countable = true
1463path = Screen+/ScreenAcquisition+
1464description = describes an acquisition run for a screen
1465
1466[ScreenAcquisition 2003FC]
1467path = -
1468
1469#[ScreenAcquisition WellSampleRef]
1470
1471[ScreenAcquisition ID]
1472type = String
1473getter = getNodeID
1474setter = setNodeID
1475description = unique label identifying the screen's acquisition run
1476
1477[ScreenAcquisition EndTime]
1478type = String
1479description = time when the last image was acquired
1480
1481[ScreenAcquisition StartTime]
1482type = String
1483description = time when the first image was acquired
1484
1485## Well ##
1486
1487[Well]
1488countable = true
1489path = Plate+/Well+
1490description = describes a Well (part of a plate)
1491
1492[Well 2003FC]
1493path = -
1494
1495#[Well ReagentRef]
1496#type = String
1497#description = label reference for the associated reagent
1498
1499[Well ID]
1500type = String
1501getter = getNodeID
1502setter = setNodeID
1503description = unique label identifying the well
1504
1505[Well Column]
1506type = Integer
1507description = column index of the well, where top-left is 0
1508
1509[Well ExternalDescription]
1510type = String
1511description = description of the externally defined ID for this plate
1512
1513[Well ExternalIdentifier]
1514type = String
1515description = reference to this well in an external database
1516
1517[Well Row]
1518type = Integer
1519description = row index of the well, where top-left is 0
1520
1521[Well Type]
1522type = String
1523description = human-readable identifier of the screen status, e.g. empty, control
1524
1525## WellSample ##
1526
1527[WellSample]
1528countable = true
1529path = Plate+/Well+/WellSample+
1530description = individual image within a Well
1531
1532[WellSample 2003FC]
1533path = -
1534
1535#[WellSample ImageRef]
1536#type = String
1537#description = label reference for the associated image
1538
1539[WellSample ID]
1540type = String
1541getter = getNodeID
1542setter = setNodeID
1543description = unique label identifying the individual well image
1544
1545[WellSample Index]
1546type = Integer
1547description = link to the Image element
1548
1549[WellSample PosX]
1550type = Float
1551description = X position of the image within the well
1552
1553[WellSample PosY]
1554type = Float
1555description = Y position of the image within the well
1556
1557[WellSample Timepoint]
1558type = Integer
1559description = time-point at which the image started to be collected
1560
1561## ImageRef ##
1562
1563#[ImageRef]
1564#countable = true
1565#path = ImageRef+
1566#description = reference to an Image element
1567
1568#[ImageRef 2003FC]
1569#path = -
1570
1571#[ImageRef ID]
1572#type = String
1573#getter = getNodeID
1574#setter = setNodeID
1575#description = TODO
1576
1577## WellSampleRef ##
1578
1579#[WellSampleRef]
1580#countable = true
1581#path = WellSampleRef+
1582#description = reference to a WellSample element
1583
1584#[WellSampleRef 2003FC]
1585#path = -
1586
1587#[WellSampleRef ID]
1588#type = String
1589#getter = getNodeID
1590#setter = setNodeID
1591#description = TODO
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