source: trunk/loci/formats/auto/entities.txt @ 4117

Revision 4117, 28.8 KB checked in by melissa, 12 years ago (diff)

Changed signatures for set*Ref and get*Ref - instead of setting/getting the referenced node's index, we now set/get the referenced node's ID.

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 = TODO
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 = TODO
58
59## Pixels ##
60
61[Pixels]
62countable = true
63path = Image+/Pixels+
64description = A pixels set in the metadata store.
65
66[Pixels ID]
67type = String
68getter = getNodeID
69setter = setNodeID
70description = TODO
71
72[Pixels SizeX]
73type = Integer
74description = The size of an individual plane or section's X axis (width).
75
76[Pixels SizeY]
77type = Integer
78description = The size of an individual plane or section's Y axis (height).
79
80[Pixels SizeZ]
81type = Integer
82description = number of optical sections per stack
83
84[Pixels SizeC]
85type = Integer
86description = number of channels per timepoint
87
88[Pixels SizeT]
89type = Integer
90description = number of timepoints
91
92[Pixels PixelType]
93type = String
94description = the pixel type
95
96[Pixels BigEndian]
97type = Boolean
98description = endianness of the pixels set
99
100[Pixels DimensionOrder]
101type = String
102description = the dimension order of the pixels set
103
104## TiffData ##
105
106[TiffData]
107countable = true
108path = Image+/Pixels+/TiffData+
109description = TODO
110
111[TiffData FirstZ]
112type = Integer
113description = TODO
114
115[TiffData FirstT]
116type = Integer
117description = TODO
118
119[TiffData FirstC]
120type = Integer
121description = TODO
122
123[TiffData IFD]
124type = Integer
125description = TODO
126
127[TiffData NumPlanes]
128type = Integer
129description = TODO
130
131[TiffData UUID]
132path = Image+/Pixels+/TiffData+/UUID
133type = String
134getter = getCData
135setter = setCData
136description = TODO
137
138[TiffData UUID 200706]
139path = -
140
141[TiffData UUID 2003FC]
142path = -
143
144[TiffData FileName]
145path = Image+/Pixels+/TiffData+/UUID
146type = String
147description = TODO
148
149[TiffData FileName 200706]
150path = -
151
152[TiffData FileName 2003FC]
153path = -
154
155## Dimensions ##
156
157[Dimensions]
158path = Image+/Pixels+
159description = a set of pixel dimensions in the metadata store \
160              with a particular index
161#notes = Unless both values are non-null, the MetadataStore should assume \
162#        physicalSizeX equals physicalSizeY (i.e., should populate the null \
163#        field with the other field's value).
164# TODO Does Bio-Formats still rely on the above requirement?
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 = TODO
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 = Integer
323description = the size of the pinhole
324
325[LogicalChannel PhotometricInterpretation]
326type = String
327description = the photometric interpretation type
328
329[LogicalChannel Mode]
330type = String
331description = the acquisition mode
332
333[LogicalChannel ContrastMethod]
334type = String
335description = the constrast method name
336
337[LogicalChannel ExWave]
338type = Integer
339description = the excitation wavelength
340
341[LogicalChannel EmWave]
342type = Integer
343description = the emission wavelength
344
345[LogicalChannel Fluor]
346type = String
347description = the fluorescence type
348
349[LogicalChannel NdFilter]
350type = Float
351description = the neutral-density filter value
352
353[LogicalChannel NdFilter 2003FC]
354getter = getNDfilter
355setter = setNDfilter
356
357[LogicalChannel PockelCellSetting]
358type = Integer
359description = TODO
360
361[LogicalChannel PockelCellSetting 2003FC]
362path = -
363
364## ChannelComponent ##
365
366[ChannelComponent]
367countable = true
368path = Image+/LogicalChannel+/ChannelComponent+
369description = a channel component describes how each channel \
370              in the pixel array relates to the logical channels
371
372[ChannelComponent 2003FC]
373path = Image+/ChannelInfo+/ChannelComponent+
374
375[ChannelComponent Index]
376type = Integer
377description = the index into the channel dimension of the 5-D pixel array
378
379[ChannelComponent ColorDomain]
380type = String
381description = which color channel this ChannelComponent belongs to \
382              (for example, 'R' for an 'RGB' PhotometricInterpretation)
383
384# FIXME xsd-fu needs to include get/setPixels methods in ChannelComponentNode?
385#[ChannelComponent Pixels]
386#type = String
387#description = the pixels to which this channel component corresponds
388
389## DisplayOptions ##
390
391[DisplayOptions]
392path = Image+/DisplayOptions
393description = various display options for a particular pixels set
394
395[DisplayOptions ID]
396type = String
397getter = getNodeID
398setter = setNodeID
399description = TODO
400
401# FIXME xsd-fu needs to include get/setPixels methods in DisplayOptionsNode
402#[DisplayOptions Pixels]
403#type = String
404#description = the pixels to which these display options correspond
405
406[DisplayOptions Zoom]
407type = Float
408description = zoom factor for use in the display (NOT THE LENS ZOOM)
409
410## RedChannel ##
411
412# FIXME xsd-fu needs to include RedChannelNode (extension of ChannelSpecNode)
413#[RedChannel]
414#path = Image+/DisplayOptions/RedChannel
415#description = information about the red channel for a particular image
416#
417# FIXME the 2003FC path below will cause compilation errors because RedChannel
418# is not of type RedChannelNode, but DisplayChannelNode; need a notation to
419# specify the distinction between node type and method getter name
420#[RedChannel 2003FC]
421#path = Image+/CA/DisplayOptions/RedChannel
422#
423#[RedChannel ChannelNumber]
424#type = Integer
425#description = TODO
426#
427#[RedChannel WhiteLevel]
428#type = Float
429#description = TODO
430#
431#[RedChannel BlackLevel]
432#type = Float
433#description = TODO
434#
435#[RedChannel Gamma]
436#type = Float
437#description = TODO
438
439## RedChannelToggle ##
440
441# FIXME xsd-fu needs to include RedChannelNode (extension of ChannelSpecNode)
442#[RedChannelToggle]
443#description = visibility toggle for a particular image's red channel
444#path = Image+/DisplayOptions/RedChannel
445#
446#[RedChannelToggle 2003FC]
447#path = Image+/CA/DisplayOptions
448#
449#[RedChannelToggle Enabled]
450#type = Boolean
451#getter = getisOn
452#setter = setisOn
453#description = indicator for whether red channel is active in the display
454#
455#[RedChannelToggle Enabled 2003FC
456#getter = isRedChannelOn
457#setter = setRedChannelOn
458
459## GreenChannel ##
460
461# FIXME xsd-fu needs to include GreenChannelNode (extension of ChannelSpecNode)
462#[GreenChannel]
463#path = Image+/DisplayOptions/GreenChannel
464#description = information about the green channel for a particular image
465#
466# FIXME the 2003FC path below will cause compilation errors because GreenChannel
467# is not of type GreenChannelNode, but DisplayChannelNode; need a notation to
468# specify the distinction between node type and method getter name
469#[GreenChannel 2003FC]
470#path = Image+/CA/DisplayOptions/GreenChannel
471#
472#[GreenChannel ChannelNumber]
473#type = Integer
474#description = TODO
475#
476#[GreenChannel WhiteLevel]
477#type = Float
478#description = TODO
479#
480#[GreenChannel BlackLevel]
481#type = Float
482#description = TODO
483#
484#[GreenChannel Gamma]
485#type = Float
486#description = TODO
487
488## GreenChannelToggle ##
489
490# FIXME xsd-fu needs to include GreenChannelNode (extension of ChannelSpecNode)
491#[GreenChannelToggle]
492#description = visibility toggle for a particular image's green channel
493#path = Image+/DisplayOptions/GreenChannel
494#
495#[GreenChannelToggle 2003FC]
496#path = Image+/CA/DisplayOptions
497#
498#[GreenChannelToggle Enabled]
499#type = Boolean
500#getter = getisOn
501#setter = setisOn
502#description = indicator for whether Green channel is active in the display
503#
504#[GreenChannelToggle Enabled 2003FC
505#getter = isGreenChannelOn
506#setter = setGreenChannelOn
507
508## BlueChannel ##
509
510# FIXME xsd-fu needs to include BlueChannelNode (extension of ChannelSpecNode)
511#[BlueChannel]
512#path = Image+/DisplayOptions/BlueChannel
513#description = information about the blue channel for a particular image
514#
515# FIXME the 2003FC path below will cause compilation errors because BlueChannel
516# is not of type BlueChannelNode, but DisplayChannelNode; need a notation to
517# specify the distinction between node type and method getter name
518#[BlueChannel 2003FC]
519#path = Image+/CA/DisplayOptions/BlueChannel
520#
521#[BlueChannel ChannelNumber]
522#type = Integer
523#description = TODO
524#
525#[BlueChannel WhiteLevel]
526#type = Float
527#description = TODO
528#
529#[BlueChannel BlackLevel]
530#type = Float
531#description = TODO
532#
533#[BlueChannel Gamma]
534#type = Float
535#description = TODO
536
537## BlueChannelToggle ##
538
539# FIXME xsd-fu needs to include BlueChannelNode (extension of ChannelSpecNode)
540#[BlueChannelToggle]
541#description = visibility toggle for a particular image's blue channel
542#path = Image+/DisplayOptions/BlueChannel
543#
544#[BlueChannelToggle 2003FC]
545#path = Image+/CA/DisplayOptions
546#
547#[BlueChannelToggle Enabled]
548#type = Boolean
549#getter = getisOn
550#setter = setisOn
551#description = indicator for whether red channel is active in the display
552#
553#[BlueChannelToggle Enabled 2003FC
554#getter = isBlueChannelOn
555#setter = setBlueChannelOn
556
557## GreyChannel ##
558
559# FIXME xsd-fu needs to include GreyChannelNode
560#[GreyChannel]
561#path = Image+/DisplayOptions/GreyChannel
562#description = information about the grey channel for a particular image
563#
564# FIXME the 2003FC path below will cause compilation errors because
565# GreyChannel is not of type GreyChannelNode, but DisplayChannelNode; need a
566# notation to specify the distinction between node type and method getter name
567#[GreyChannel 2003FC]
568#path = Image+/CA/DisplayOptions/GreyChannel
569#
570#[GreyChannel ChannelNumber]
571#type = Integer
572#description = TODO
573#
574#[GreyChannel WhiteLevel]
575#type = Float
576#description = TODO
577#
578#[GreyChannel BlackLevel]
579#type = Float
580#description = TODO
581#
582#[GreyChannel Gamma]
583#type = Float
584#description = TODO
585
586## GreyChannelMap ##
587
588# FIXME xsd-fu needs to include GreyChannelNode
589#[GreyChannelMap]
590#path = Image+/DisplayOptions/GreyChannel
591#description = color map setting for a particular image's grey channel
592#
593#[GreyChannelMap 2003FC]
594#path = Image+/CA/DisplayOptions
595#
596#[GreyChannelMap ColorMap]
597#type = String
598#description = TODO
599#
600# FIXME need to implement this conversion method in OMEXMLNode
601#[GreyChannelMap ColorMap 2003FC]
602#type = Boolean
603#getter = isDisplayRGB
604#setter = setDisplayRGB
605
606## DisplayOptionsProjection ##
607
608[DisplayOptionsProjection]
609path = Image+/DisplayOptions/Projection
610description = maximum intensity projection-related display options \
611              for a particular image
612
613[DisplayOptionsProjection ZStart]
614type = Integer
615description = the first focal plane to include \
616              in the maximum intensity projection
617
618[DisplayOptionsProjection ZStart 2003FC]
619getter = getZstart
620setter = setZstart
621
622[DisplayOptionsProjection ZStop]
623type = Integer
624description = the last focal plane to include \
625              in the maximum intensity projection
626
627[DisplayOptionsProjection ZStop 2003FC]
628getter = getZstop
629setter = setZstop
630
631## DisplayOptionsTime ##
632
633[DisplayOptionsTime]
634path = Image+/DisplayOptions/Time
635description = time range-related display options for a particular image
636
637[DisplayOptionsTime TStart]
638type = Integer
639description = the first time point to include in the animation
640
641[DisplayOptionsTime TStart 2003FC]
642getter = getTstart
643setter = setTstart
644
645[DisplayOptionsTime TStop]
646type = Integer
647description = the last time point to include in the animation
648
649[DisplayOptionsTime TStop 2003FC]
650getter = getTstop
651setter = setTstop
652
653## ROI ##
654
655[ROI]
656countable = true
657path = Image+/DisplayOptions/ROI+
658description = a 5D bounding box region of interest in the metadata store \
659              with a particular index
660
661[ROI ID]
662type = String
663getter = getNodeID
664setter = setNodeID
665description = TODO
666
667[ROI X0]
668type = Integer
669description = the starting X coordinate
670
671[ROI Y0]
672type = Integer
673description = the starting Y coordinate
674
675[ROI X1]
676type = Integer
677description = the ending X coordinate
678
679[ROI Y1]
680type = Integer
681description = the ending Y coordinate
682
683[ROI Z0]
684type = Integer
685description = the starting Z coordinate
686
687[ROI Z1]
688type = Integer
689description = the ending Z coordinate
690
691[ROI T0]
692type = Integer
693description = the starting timepoint
694
695[ROI T1]
696type = Integer
697description = the ending timepoint
698
699### Entities for Instrument settings for a particular Image ###
700
701## DetectorSettings ##
702
703[DetectorSettings]
704path = Image+/LogicalChannel+/DetectorRef
705description = the detector associated with a particular logical channel
706
707[DetectorSettings 2003FC]
708path = Image+/ChannelInfo+/DetectorRef
709
710[DetectorSettings Detector]
711type = String
712getter = getNodeID
713setter = setNodeID
714description = the detector associated with this channel
715
716[DetectorSettings Offset]
717type = Float
718description = the detector offset
719
720[DetectorSettings Gain]
721type = Float
722description = the detector gain
723
724## LightSourceSettings ##
725
726[LightSourceSettings]
727path = Image+/LogicalChannel+/LightSourceRef
728description = the light source associated with a particular logical channel
729
730[LightSourceSettings 2003FC]
731path = Image+/ChannelInfo+/LightSourceRef
732
733[LightSourceSettings LightSource]
734type = String
735getter = getNodeID
736setter = setNodeID
737description = the primary light source
738
739[LightSourceSettings Attenuation]
740type = Float
741description = the primary light source attenuation
742
743[LightSourceSettings Wavelength]
744type = Integer
745description = the primary light source wavelength
746
747### Entities for other Image-specific information ###
748
749## StageLabel ##
750
751[StageLabel]
752path = Image+/StageLabel
753description = a stage label in the metadata store with a particular index
754
755[StageLabel Name]
756type = String
757description = a name for the stage label
758
759[StageLabel X]
760type = Float
761description = the x coordinate of the stage
762
763[StageLabel Y]
764type = Float
765description = the y coordinate of the stage
766
767[StageLabel Z]
768type = Float
769description = the z coordinate of the stage
770
771### Entities for Instrument hardware -- these DO NOT vary by Image ###
772
773## Instrument ##
774
775[Instrument]
776countable = true
777path = Instrument+
778description = an instrument in the metadata store with a particular index
779
780[Instrument ID]
781type = String
782getter = getNodeID
783setter = setNodeID
784description = TODO
785
786## LightSource ##
787
788[LightSource]
789countable = true
790path = Instrument+/LightSource+
791description = a light source for a particular instrument
792
793[LightSource ID]
794type = String
795getter = getNodeID
796setter = setNodeID
797description = TODO
798
799[LightSource Manufacturer]
800type = String
801description = TODO
802
803[LightSource Model]
804type = String
805description = TODO
806
807[LightSource SerialNumber]
808type = String
809description = TODO
810
811[LightSource Power]
812type = Float
813description = TODO
814
815[LightSource Power 200706]
816path = -
817
818[LightSource Power 2003FC]
819path = -
820
821## Laser ##
822
823[Laser]
824path = Instrument+/LightSource+/Laser
825description = a laser for a particular instrument
826
827[Laser Type]
828type = String
829description = TODO
830
831[Laser LaserMedium]
832type = String
833description = TODO
834
835[Laser LaserMedium 2003FC]
836getter = getMedium
837setter = setMedium
838
839[Laser Wavelength]
840type = Integer
841description = TODO
842
843[Laser FrequencyMultiplication]
844type = Integer
845description = TODO
846
847[Laser FrequencyMultiplication 2003FC]
848type = Boolean
849getter = getFrequencyDoubled
850setter = setFrequencyDoubled
851
852[Laser Tuneable]
853type = Boolean
854description = TODO
855
856[Laser Tuneable 2003FC]
857getter = getTunable
858setter = setTunable
859
860[Laser Pulse]
861type = String
862description = TODO
863
864## Filament ##
865
866[Filament]
867path = Instrument+/LightSource+/Filament
868description = a filament for a particular instrument
869
870[Filament Type]
871type = String
872description = TODO
873
874## Arc ##
875
876[Arc]
877path = Instrument+/LightSource+/Arc
878description = an arc for a particular instrument
879
880[Arc Type]
881type = String
882description = TODO
883
884## Detector ##
885
886[Detector]
887countable = true
888path = Instrument+/Detector+
889description = a detector for a particular instrument
890
891[Detector ID]
892type = String
893getter = getNodeID
894setter = setNodeID
895description = TODO
896
897[Detector Manufacturer]
898type = String
899description = TODO
900
901[Detector Model]
902type = String
903description = TODO
904
905[Detector SerialNumber]
906type = String
907description = TODO
908
909[Detector Type]
910type = String
911description = TODO
912
913[Detector Gain]
914type = Float
915description = TODO
916
917[Detector Voltage]
918type = Float
919description = TODO
920
921[Detector Offset]
922type = Float
923description = TODO
924
925## Objective ##
926
927[Objective]
928countable = true
929path = Instrument+/Objective+
930description = an objective for a particular instrument
931
932[Objective ID]
933type = String
934getter = getNodeID
935setter = setNodeID
936description = TODO
937
938[Objective Manufacturer]
939type = String
940description = TODO
941
942[Objective Model]
943type = String
944description = TODO
945
946[Objective SerialNumber]
947type = String
948description = TODO
949
950[Objective Correction]
951type = String
952description = TODO
953
954[Objective Correction 2003FC]
955path = -
956
957[Objective Immersion]
958type = String
959description = TODO
960
961[Objective Immersion 2003FC]
962path = -
963
964[Objective LensNA]
965type = Float
966description = TODO
967
968[Objective NominalMagnification]
969type = Integer
970description = TODO
971
972[Objective NominalMagnification 2003FC]
973path = -
974
975[Objective CalibratedMagnification]
976type = Float
977description = TODO
978
979[Objective CalibratedMagnification 2003FC]
980getter = getMagnification
981setter = setMagnification
982
983[Objective WorkingDistance]
984type = Float
985description = TODO
986
987[Objective WorkingDistance 2003FC]
988path = -
989
990#TODO figure out how to reconcile the two filter models
991
992#http://www.openmicroscopy.org/Schemas/OME/2007-06/ome.xsd
993#http://ome-xml.org/wiki/FilterAndFilterSet
994
995#http://www.openmicroscopy.org/XMLschemas/OME/FC/ome.xsd
996#http://openmicroscopy.org/api/xml/OME/ome-instrument.html
997
998## ExcitationFilter ##
999
1000#[ExcitationFilter]
1001#path = ?
1002#description = an excitation filter for a particular instrument
1003#
1004#[ExcitationFilter 2003FC]
1005#path = CA/ExcitationFilter+
1006#
1007#[ExcitationFilter Manufacturer]
1008#type = String
1009#description = TODO
1010#
1011#[ExcitationFilter Model]
1012#type = String
1013#description = TODO
1014#
1015#[ExcitationFilter LotNumber]
1016#type = String
1017#description = TODO
1018#
1019#[ExcitationFilter Type]
1020#type = String
1021#description = TODO
1022
1023## Dichroic ##
1024
1025#[Dichroic]
1026#path = ?
1027#description = a dichroic for a particular instrument
1028#
1029#[Dichroic 2003FC]
1030#path = CA/Dichroic+
1031#
1032#[Dichroic Manufacturer]
1033#type = String
1034#description = TODO
1035#
1036#[Dichroic Model]
1037#type = String
1038#description = TODO
1039#
1040#[Dichroic LotNumber]
1041#type = String
1042#description = TODO
1043
1044## EmissionFilter ##
1045
1046#[EmissionFilter]
1047#path = ?
1048#description = an emission filter for a particular instrument
1049#
1050#[EmissionFilter 2003FC]
1051#path = CA/EmissionFilter+
1052#
1053#[EmissionFilter Manufacturer]
1054#type = String
1055#description = TODO
1056#
1057#[EmissionFilter Model]
1058#type = String
1059#description = TODO
1060#
1061#[EmissionFilter LotNumber]
1062#type = String
1063#description = TODO
1064#
1065#[EmissionFilter Type]
1066#type = String
1067#description = TODO
1068
1069## FilterSet ##
1070
1071#[FilterSet]
1072#path = ?
1073#description = a filter set for a particular instrument
1074#
1075#[FilterSet 2003FC]
1076#path = CA/FilterSet+
1077#
1078#[FilterSet Manufacturer]
1079#type = String
1080#description = TODO
1081#
1082#[FilterSet Model]
1083#type = String
1084#description = TODO
1085#
1086#[FilterSet LotNumber]
1087#type = String
1088#description = TODO
1089
1090## OTF ##
1091
1092[OTF]
1093countable = true
1094path = Instrument+/OTF+
1095description = an optical transfer function for a particular instrument
1096
1097[OTF ID]
1098type = String
1099getter = getNodeID
1100setter = setNodeID
1101description = TODO
1102
1103[OTF SizeX]
1104type = Integer
1105description = TODO
1106
1107[OTF SizeY]
1108type = Integer
1109description = TODO
1110
1111[OTF PixelType]
1112type = String
1113description = TODO
1114
1115[OTF OpticalAxisAveraged]
1116type = Boolean
1117description = TODO
1118
1119[OTF OpticalAxisAveraged 2003FC]
1120getter = getOpticalAxisAvrg
1121setter = setOpticalAxisAvrg
1122
1123### Entities for Experimenter details ###
1124
1125## Experimenter ##
1126
1127[Experimenter]
1128countable = true
1129path = Experimenter+
1130description = an experimenter in the metadata store with a particular index
1131
1132[Experimenter ID]
1133type = String
1134getter = getNodeID
1135setter = setNodeID
1136description = TODO
1137
1138[Experimenter FirstName]
1139type = String
1140description = the first name of the experimenter
1141
1142[Experimenter LastName]
1143type = String
1144description = the last name of the experimenter
1145
1146[Experimenter Email]
1147type = String
1148description = the e-mail address of the experimenter
1149
1150[Experimenter Institution]
1151type = String
1152description = the institution to which the experimenter belongs
1153
1154### Entities for high-content screening ###
1155
1156## Plate ##
1157
1158[Plate]
1159countable = true
1160path = Plate+
1161description = identifies a plate within a screen
1162
1163[Plate 2003FC]
1164path = -
1165
1166[Plate ID]
1167type = String
1168getter = getNodeID
1169setter = setNodeID
1170description = TODO
1171
1172#[Plate ScreenRef]
1173#type =
1174#description = TODO
1175
1176#[Plate Well]
1177#type = Integer
1178#description = TODO
1179
1180[Plate Name]
1181type = String
1182description = the plate's name
1183
1184[Plate Description]
1185type = String
1186
1187[Plate Status]
1188type = String
1189description = current state of the plate with respect to the experiment work-flow
1190
1191[Plate ExternalIdentifier]
1192type = String
1193description = reference to this plate in an external database
1194
1195## PlateRef ##
1196
1197[PlateRef]
1198countable = true
1199path = Screen+/PlateRef+
1200description = reference to a Plate element
1201
1202[PlateRef 2003FC]
1203path = -
1204
1205[PlateRef ID]
1206type = String
1207getter = getNodeID
1208setter = setNodeID
1209description = TODO
1210
1211## Reagent ##
1212
1213[Reagent]
1214countable = true
1215path = Screen+/Reagent+
1216description = describes a chemical or other physical experimental parameter
1217
1218[Reagent 2003FC]
1219path = -
1220
1221[Reagent ID]
1222type = String
1223getter = getNodeID
1224setter = setNodeID
1225description = TODO
1226
1227[Reagent Description]
1228type = String
1229description = the reagent's description
1230
1231[Reagent Name]
1232type = String
1233description = the reagent's name
1234
1235[Reagent ReagentIdentifier]
1236type = String
1237description = reference to this reagent in an external database
1238
1239## ReagentRef ##
1240
1241#[ReagentRef]
1242#countable = true
1243#path = Screen+/ReagentRef+
1244#description = reference to a Reagent
1245
1246#[ReagentRef 2003FC]
1247#path = -
1248
1249#[ReagentRef ID]
1250#type = String
1251#getter = getNodeID
1252#setter = setNodeID
1253#description = TODO
1254
1255## Screen ##
1256
1257[Screen]
1258countable = true
1259path = Screen+
1260description = description of a screen (grouping of plates)
1261
1262[Screen 2003FC]
1263path = -
1264
1265#[Screen Reagent]
1266#type = String
1267#description = TODO
1268
1269#[Screen PlateRef]
1270#type = String
1271#description = TODO
1272
1273#[Screen ScreenAcquisition]
1274
1275[Screen ID]
1276type = String
1277getter = getNodeID
1278setter = setNodeID
1279description = TODO
1280
1281[Screen Name]
1282type = String
1283description = the screen's name
1284
1285[Screen ProtocolIdentifier]
1286type = String
1287description = reference to an externally defined protocol
1288
1289[Screen ProtocolDescription]
1290type = String
1291description = description of the screen's protocol
1292
1293[Screen ReagentSetDescription]
1294type = String
1295description = description of a set of reagents
1296
1297#[Screen ReagentSetidentifier]
1298#type = String
1299#description = reference to an externally defined set of reagents
1300
1301[Screen Type]
1302type = String
1303description = human-readable screen type, e.g. RNAi, cDNA
1304
1305## ScreenRef ##
1306
1307#[ScreenRef]
1308#countable = true
1309#path = Screen+/ScreenRef+
1310#description = reference to a Screen element
1311
1312#[ScreenRef 2003FC]
1313#path = -
1314
1315#[ScreenRef ID]
1316#type = String
1317#getter = getNodeID
1318#setter = setNodeID
1319#description = TODO
1320
1321## ScreenAcquisition ##
1322
1323[ScreenAcquisition]
1324countable = true
1325path = Screen+/ScreenAcquisition+
1326description = describes an acquisition run for a screen
1327
1328[ScreenAcquisition 2003FC]
1329path = -
1330
1331#[ScreenAcquisition WellSampleRef]
1332
1333[ScreenAcquisition ID]
1334type = String
1335getter = getNodeID
1336setter = setNodeID
1337description = TODO
1338
1339[ScreenAcquisition EndTime]
1340type = String
1341description = time when the last image was acquired
1342
1343[ScreenAcquisition StartTime]
1344type = String
1345description = time when the first image was acquired
1346
1347## Well ##
1348
1349[Well]
1350countable = true
1351path = Well+
1352description = describes a Well (part of a plate)
1353
1354[Well 2003FC]
1355path = -
1356
1357#[Well WellSample]
1358#type = String
1359#description = TODO
1360
1361#[Well ReagentRef]
1362#type = String
1363#description = TODO
1364
1365[Well ID]
1366type = String
1367getter = getNodeID
1368setter = setNodeID
1369description = TODO
1370
1371[Well Column]
1372type = Integer
1373description = column index of the well, where top-left is 0
1374
1375[Well ExternalDescription]
1376type = String
1377description = description of the externally defined ID for this plate
1378
1379[Well ExternalIdentifier]
1380type = String
1381description = reference to this well in an external database
1382
1383[Well Row]
1384type = Integer
1385description = row index of the well, where top-left is 0
1386
1387[Well Type]
1388type = String
1389description = human-readable identifier of the screen status, e.g. empty, control
1390
1391## WellSample ##
1392
1393[WellSample]
1394countable = true
1395path = Well+/WellSample+
1396description = individual image within a Well
1397
1398[WellSample 2003FC]
1399path = -
1400
1401#[WellSample ImageRef]
1402#type = String
1403#description = TODO
1404
1405[WellSample ID]
1406type = String
1407getter = getNodeID
1408setter = setNodeID
1409description = TODO
1410
1411[WellSample Index]
1412type = Integer
1413description = link to the Image element
1414
1415[WellSample PosX]
1416type = Float
1417description = X position of the image within the well
1418
1419[WellSample PosY]
1420type = Float
1421description = Y position of the image within the well
1422
1423[WellSample Timepoint]
1424type = Integer
1425description = time-point at which the image started to be collected
1426
1427## ImageRef ##
1428
1429#[ImageRef]
1430#countable = true
1431#path = ImageRef+
1432#description = reference to an Image element
1433
1434#[ImageRef 2003FC]
1435#path = -
1436
1437#[ImageRef ID]
1438#type = String
1439#getter = getNodeID
1440#setter = setNodeID
1441#description = TODO
1442
1443## WellSampleRef ##
1444
1445#[WellSampleRef]
1446#countable = true
1447#path = WellSampleRef+
1448#description = reference to a WellSample element
1449
1450#[WellSampleRef 2003FC]
1451#path = -
1452
1453#[WellSampleRef ID]
1454#type = String
1455#getter = getNodeID
1456#setter = setNodeID
1457#description = TODO
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