source: trunk/components/bio-formats-auto/src/entities.txt @ 4638

Revision 4638, 31.9 KB checked in by melissa, 12 years ago (diff)

Updated DetectorSettings entities and added ObjectiveSettings entities.

Line 
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#TODO figure out how to reconcile the two filter models
1071
1072#http://www.openmicroscopy.org/Schemas/OME/2007-06/ome.xsd
1073#http://ome-xml.org/wiki/FilterAndFilterSet
1074
1075#http://www.openmicroscopy.org/XMLschemas/OME/FC/ome.xsd
1076#http://openmicroscopy.org/api/xml/OME/ome-instrument.html
1077
1078## ExcitationFilter ##
1079
1080#[ExcitationFilter]
1081#path = ?
1082#description = an excitation filter for a particular instrument
1083#
1084#[ExcitationFilter 2003FC]
1085#path = CA/ExcitationFilter+
1086#
1087#[ExcitationFilter Manufacturer]
1088#type = String
1089#description = TODO
1090#
1091#[ExcitationFilter Model]
1092#type = String
1093#description = TODO
1094#
1095#[ExcitationFilter LotNumber]
1096#type = String
1097#description = TODO
1098#
1099#[ExcitationFilter Type]
1100#type = String
1101#description = TODO
1102
1103## Dichroic ##
1104
1105#[Dichroic]
1106#path = ?
1107#description = a dichroic for a particular instrument
1108#
1109#[Dichroic 2003FC]
1110#path = CA/Dichroic+
1111#
1112#[Dichroic Manufacturer]
1113#type = String
1114#description = TODO
1115#
1116#[Dichroic Model]
1117#type = String
1118#description = TODO
1119#
1120#[Dichroic LotNumber]
1121#type = String
1122#description = TODO
1123
1124## EmissionFilter ##
1125
1126#[EmissionFilter]
1127#path = ?
1128#description = an emission filter for a particular instrument
1129#
1130#[EmissionFilter 2003FC]
1131#path = CA/EmissionFilter+
1132#
1133#[EmissionFilter Manufacturer]
1134#type = String
1135#description = TODO
1136#
1137#[EmissionFilter Model]
1138#type = String
1139#description = TODO
1140#
1141#[EmissionFilter LotNumber]
1142#type = String
1143#description = TODO
1144#
1145#[EmissionFilter Type]
1146#type = String
1147#description = TODO
1148
1149## FilterSet ##
1150
1151#[FilterSet]
1152#path = ?
1153#description = a filter set for a particular instrument
1154#
1155#[FilterSet 2003FC]
1156#path = CA/FilterSet+
1157#
1158#[FilterSet Manufacturer]
1159#type = String
1160#description = TODO
1161#
1162#[FilterSet Model]
1163#type = String
1164#description = TODO
1165#
1166#[FilterSet LotNumber]
1167#type = String
1168#description = TODO
1169
1170## OTF ##
1171
1172[OTF]
1173countable = true
1174path = Instrument+/OTF+
1175description = an optical transfer function for a particular instrument
1176
1177[OTF ID]
1178type = String
1179getter = getNodeID
1180setter = setNodeID
1181description = unique label identifying the optical transfer function
1182
1183[OTF SizeX]
1184type = Integer
1185description = TODO
1186
1187[OTF SizeY]
1188type = Integer
1189description = TODO
1190
1191[OTF PixelType]
1192type = String
1193description = TODO
1194
1195[OTF OpticalAxisAveraged]
1196type = Boolean
1197description = TODO
1198
1199[OTF OpticalAxisAveraged 2003FC]
1200getter = getOpticalAxisAvrg
1201setter = setOpticalAxisAvrg
1202
1203[OTF Objective]
1204path = Instrument+/OTF+/ObjectiveRef
1205type = String
1206getter = getNodeID
1207setter = setNodeID
1208description = objective described by the optical transfer function
1209
1210### Entities for Experiment & Experimenter details ###
1211
1212## Experiment ##
1213
1214[Experiment]
1215countable = true
1216path = Experiment+
1217description = information about a particular experiment
1218
1219[Experiment ID]
1220type = String
1221getter = getNodeID
1222setter = setNodeID
1223description = unique label identifying the experiment
1224
1225[Experiment Description]
1226type = String
1227description = TODO
1228
1229[Experiment Type]
1230type = String
1231description = TODO
1232
1233#[Experiment Experimenter]
1234#TODO - need Experiment.setExperimenter in OME-XML Java library
1235
1236## Experimenter ##
1237
1238[Experimenter]
1239countable = true
1240path = Experimenter+
1241description = information about someone performing an experiment
1242
1243[Experimenter ID]
1244type = String
1245getter = getNodeID
1246setter = setNodeID
1247description = unique label identifying the experimenter
1248
1249[Experimenter FirstName]
1250type = String
1251description = the first name of the experimenter
1252
1253[Experimenter LastName]
1254type = String
1255description = the last name of the experimenter
1256
1257[Experimenter Email]
1258type = String
1259description = the e-mail address of the experimenter
1260
1261[Experimenter Institution]
1262type = String
1263description = the institution to which the experimenter belongs
1264
1265## GroupRef ##
1266
1267[GroupRef]
1268countable = true
1269path = Experimenter+/GroupRef+
1270description = HACK - force creation of MetadataRetrieve.getGroupRefCount(int)
1271
1272## ExperimenterMembership ##
1273
1274[ExperimenterMembership]
1275countable = true
1276path = Experimenter+/GroupRef+
1277description = a linkage between a particular experimenter and a group
1278
1279[ExperimenterMembership Group]
1280type = String
1281getter = getNodeID
1282setter = setNodeID
1283description = the group associated with this membership
1284
1285### Entities for high-content screening ###
1286
1287## Plate ##
1288
1289[Plate]
1290countable = true
1291path = Plate+
1292description = identifies a plate within a screen
1293
1294[Plate 2003FC]
1295path = -
1296
1297[Plate ID]
1298type = String
1299getter = getNodeID
1300setter = setNodeID
1301description = unique label identifying the plate
1302
1303#[Plate ScreenRef]
1304#type =
1305#description = TODO
1306
1307[Plate Name]
1308type = String
1309description = the plate's name
1310
1311[Plate Description]
1312type = String
1313
1314[Plate Status]
1315type = String
1316description = current state of the plate with respect to the experiment work-flow
1317
1318[Plate ExternalIdentifier]
1319type = String
1320description = reference to this plate in an external database
1321
1322## PlateRef ##
1323
1324[PlateRef]
1325countable = true
1326path = Screen+/PlateRef+
1327description = reference to a Plate element
1328
1329[PlateRef 2003FC]
1330path = -
1331
1332[PlateRef ID]
1333type = String
1334getter = getNodeID
1335setter = setNodeID
1336description = label reference for the associated plate
1337
1338## Reagent ##
1339
1340[Reagent]
1341countable = true
1342path = Screen+/Reagent+
1343description = describes a chemical or other physical experimental parameter
1344
1345[Reagent 2003FC]
1346path = -
1347
1348[Reagent ID]
1349type = String
1350getter = getNodeID
1351setter = setNodeID
1352description = unique label identifying the reagent
1353
1354[Reagent Description]
1355type = String
1356description = the reagent's description
1357
1358[Reagent Name]
1359type = String
1360description = the reagent's name
1361
1362[Reagent ReagentIdentifier]
1363type = String
1364description = reference to this reagent in an external database
1365
1366## ReagentRef ##
1367
1368#[ReagentRef]
1369#countable = true
1370#path = Screen+/ReagentRef+
1371#description = reference to a Reagent
1372
1373#[ReagentRef 2003FC]
1374#path = -
1375
1376#[ReagentRef ID]
1377#type = String
1378#getter = getNodeID
1379#setter = setNodeID
1380#description = label reference for the associated reagent
1381
1382## Screen ##
1383
1384[Screen]
1385countable = true
1386path = Screen+
1387description = description of a screen (grouping of plates)
1388
1389[Screen 2003FC]
1390path = -
1391
1392#[Screen PlateRef]
1393#type = String
1394#description = label reference for the associated plate
1395
1396[Screen ID]
1397type = String
1398getter = getNodeID
1399setter = setNodeID
1400description = unique label identifying the screen
1401
1402[Screen Name]
1403type = String
1404description = the screen's name
1405
1406[Screen ProtocolIdentifier]
1407type = String
1408description = reference to an externally defined protocol
1409
1410[Screen ProtocolDescription]
1411type = String
1412description = description of the screen's protocol
1413
1414[Screen ReagentSetDescription]
1415type = String
1416description = description of a set of reagents
1417
1418#[Screen ReagentSetidentifier]
1419#type = String
1420#description = reference to an externally defined set of reagents
1421
1422[Screen Type]
1423type = String
1424description = human-readable screen type, e.g. RNAi, cDNA
1425
1426## ScreenRef ##
1427
1428#[ScreenRef]
1429#countable = true
1430#path = Screen+/ScreenRef+
1431#description = reference to a Screen element
1432
1433#[ScreenRef 2003FC]
1434#path = -
1435
1436#[ScreenRef ID]
1437#type = String
1438#getter = getNodeID
1439#setter = setNodeID
1440#description = label reference for the associated screen
1441
1442## ScreenAcquisition ##
1443
1444[ScreenAcquisition]
1445countable = true
1446path = Screen+/ScreenAcquisition+
1447description = describes an acquisition run for a screen
1448
1449[ScreenAcquisition 2003FC]
1450path = -
1451
1452#[ScreenAcquisition WellSampleRef]
1453
1454[ScreenAcquisition ID]
1455type = String
1456getter = getNodeID
1457setter = setNodeID
1458description = unique label identifying the screen's acquisition run
1459
1460[ScreenAcquisition EndTime]
1461type = String
1462description = time when the last image was acquired
1463
1464[ScreenAcquisition StartTime]
1465type = String
1466description = time when the first image was acquired
1467
1468## Well ##
1469
1470[Well]
1471countable = true
1472path = Plate+/Well+
1473description = describes a Well (part of a plate)
1474
1475[Well 2003FC]
1476path = -
1477
1478#[Well ReagentRef]
1479#type = String
1480#description = label reference for the associated reagent
1481
1482[Well ID]
1483type = String
1484getter = getNodeID
1485setter = setNodeID
1486description = unique label identifying the well
1487
1488[Well Column]
1489type = Integer
1490description = column index of the well, where top-left is 0
1491
1492[Well ExternalDescription]
1493type = String
1494description = description of the externally defined ID for this plate
1495
1496[Well ExternalIdentifier]
1497type = String
1498description = reference to this well in an external database
1499
1500[Well Row]
1501type = Integer
1502description = row index of the well, where top-left is 0
1503
1504[Well Type]
1505type = String
1506description = human-readable identifier of the screen status, e.g. empty, control
1507
1508## WellSample ##
1509
1510[WellSample]
1511countable = true
1512path = Plate+/Well+/WellSample+
1513description = individual image within a Well
1514
1515[WellSample 2003FC]
1516path = -
1517
1518#[WellSample ImageRef]
1519#type = String
1520#description = label reference for the associated image
1521
1522[WellSample ID]
1523type = String
1524getter = getNodeID
1525setter = setNodeID
1526description = unique label identifying the individual well image
1527
1528[WellSample Index]
1529type = Integer
1530description = link to the Image element
1531
1532[WellSample PosX]
1533type = Float
1534description = X position of the image within the well
1535
1536[WellSample PosY]
1537type = Float
1538description = Y position of the image within the well
1539
1540[WellSample Timepoint]
1541type = Integer
1542description = time-point at which the image started to be collected
1543
1544## ImageRef ##
1545
1546#[ImageRef]
1547#countable = true
1548#path = ImageRef+
1549#description = reference to an Image element
1550
1551#[ImageRef 2003FC]
1552#path = -
1553
1554#[ImageRef ID]
1555#type = String
1556#getter = getNodeID
1557#setter = setNodeID
1558#description = TODO
1559
1560## WellSampleRef ##
1561
1562#[WellSampleRef]
1563#countable = true
1564#path = WellSampleRef+
1565#description = reference to a WellSample element
1566
1567#[WellSampleRef 2003FC]
1568#path = -
1569
1570#[WellSampleRef ID]
1571#type = String
1572#getter = getNodeID
1573#setter = setNodeID
1574#description = TODO
Note: See TracBrowser for help on using the repository browser.