-
Notifications
You must be signed in to change notification settings - Fork 1
/
ndx-multichannel-volume.extensions.yaml
285 lines (285 loc) · 8.2 KB
/
ndx-multichannel-volume.extensions.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
groups:
- neurodata_type_def: CElegansSubject
neurodata_type_inc: Subject
doc: Subject object with support for C. Elegans specific attributes
attributes:
- name: growth_stage_time
dtype: text
doc: amount of time in current growth stage in ISO 8601 duration format
required: false
datasets:
- name: growth_stage
dtype: text
doc: Growth stage of C. elegans. One of two-fold, three-fold, L1-L4, YA, OA, duaer,
post-dauer L4, post-dauer YA, post-dauer OA
- name: cultivation_temp
dtype: float32
doc: Worm cultivation temperature in C
quantity: '?'
- neurodata_type_def: MultiChannelVolumeSeries
neurodata_type_inc: TimeSeries
doc: Image series of volumetric data with multiple channels
attributes:
- name: scan_line_rate
dtype: float32
doc: Lines imaged per second.
required: false
- name: binning
dtype: uint8
doc: Amount of pixels combined into bins; could be 1, 2, 4, 8, etc.
required: false
- name: starting_frame
dtype: int32
dims:
- num_files
shape:
- null
doc: Each external image may contain one or more consecutive frames of the full
ImageSeries. This attribute serves as an index to indicate which frames each
file contains, to faciliate random access. The 'starting_frame' attribute, hence,
contains a list of frame numbers within the full ImageSeries of the first frame
of each file listed in the parent 'external_file' dataset. Zero-based indexing
is used (hence, the first element will always be zero). For example, if the
'external_file' dataset has three paths to files and the first file has 5 frames,
the second file has 10 frames, and the third file has 20 frames, then this attribute
will have values [0, 5, 15]. If there is a single external file that holds all
of the frames of the ImageSeries (and so there is a single element in the 'external_file'
dataset), then this attribute should have value [0].
required: false
- name: format
dtype: text
default_value: raw
doc: Format of image. If this is 'external', then the attribute 'external_file'
contains the path information to the image files. If this is 'raw', then the
raw (single-channel) binary data is stored in the 'data' dataset. If this attribute
is not present, then the default format='raw' case is assumed.
required: false
datasets:
- name: data
dtype: uint16
dims:
- - frame
- x
- y
- z
- - frame
- x
- y
- z
- channel
shape:
- - null
- null
- null
- null
- - null
- null
- null
- null
- null
doc: Data representing multichannel volumetric images across frames
- name: pmt_gain
dtype: float32
dims:
- channels
shape:
- null
doc: Photomultiplier gain for each channel
quantity: '?'
- name: exposure_time
dtype: float32
dims:
- channels
shape:
- null
doc: Exposure time of the sample, in seconds; often the inverse of the frequency.
quantity: '?'
- name: power
dtype: float32
dims:
- channels
shape:
- null
doc: Power of the excitation in mW, if known.
quantity: '?'
- name: intensity
dtype: float32
doc: Intensity of the excitation in mW/mm^2, if known.
quantity: '?'
- name: dimension
dtype: int32
dims:
- num_dims
shape:
- null
doc: Number of pixels on x, y, and z axes
- name: external_file
dtype: text
dims:
- num_files
shape:
- null
doc: Paths to one or more external file(s). Field is only present if format ='external'.
This is only relevant if the image series is stored in the file system as one
or more image file(s). This field should NOT be used if the image is stored
in another NWB file and that file is linked to this file
quantity: '?'
links:
- name: imaging_volume
target_type: ImagingVolume
doc: Link to ImagingVolume object from which this data was generated.
- name: device
target_type: Device
doc: Link to the Device object that was used to capture these images
- neurodata_type_def: MultiChannelVolume
neurodata_type_inc: NWBDataInterface
doc: An extension of the base NWBData type to allow for multichannel volumetric
images
datasets:
- name: description
dtype: text
doc: description of image
- name: RGBW_channels
dtype: int8
dims:
- channels
shape:
- 4
doc: which channels in image map to RGBW
quantity: '?'
- name: data
dtype: uint16
dims:
- x
- y
- z
- channel
shape:
- null
- null
- null
- null
doc: Volumetric multichannel data
links:
- name: imaging_volume
target_type: ImagingVolume
doc: Link to ImagingVolume object from which this data was generated.
- neurodata_type_def: ImagingVolume
neurodata_type_inc: ImagingPlane
doc: An Imaging Volume and its Metadata
groups:
- neurodata_type_inc: OpticalChannelPlus
doc: An optical channel used to record from an imaging volume
quantity: '*'
- name: order_optical_channels
neurodata_type_inc: OpticalChannelReferences
doc: Ordered list of names of the optical channels in the data
- neurodata_type_def: OpticalChannelReferences
neurodata_type_inc: NWBDataInterface
doc: wrapper for optical channel references dataset
datasets:
- name: channels
dtype: text
dims:
- NumChannels
shape:
- null
doc: Ordered list of names of optical channels. Should refer to the names of the
OpticalChannelPlus objects. ie. GCaMP, mNeptune, etc.
- neurodata_type_def: OpticalChannelPlus
neurodata_type_inc: OpticalChannel
doc: An optical channel used to record from an imaging volume. Contains both emission
and excitation bands.
datasets:
- name: emission_range
dtype: float32
dims:
- start and end
shape:
- 2
doc: boundaries of emission wavelength for channel, in nm
- name: excitation_range
dtype: float32
dims:
- start and end
shape:
- 2
doc: boundaries of excitation wavelength for channel, in nm
- name: excitation_lambda
dtype: float32
doc: Excitation wavelength for channle, in nm.
- neurodata_type_def: VolumeSegmentation
neurodata_type_inc: PlaneSegmentation
doc: Results from image segmentation of a specific imaging volume
datasets:
- name: labels
dtype: text
dims:
- num_ROI
shape:
- null
doc: Ordered list of labels for ROIs
quantity: '?'
- name: color_voxel_mask
neurodata_type_inc: VectorData
dtype:
- name: x
dtype: uint32
doc: Voxel x-coordinate
- name: y
dtype: uint32
doc: Voxel y-coordinate
- name: z
dtype: uint32
doc: Voxel z-coordinate
- name: R
dtype: uint32
doc: Voxel red value
- name: G
dtype: uint32
doc: Voxel green value
- name: B
dtype: uint32
doc: Voxel blue value
- name: W
dtype: uint32
doc: voxel white value
- name: weight
dtype: float32
doc: Weight of the voxel
doc: Voxel masks for each ROI including RGBW color values for each pixel
quantity: '?'
links:
- name: imaging_volume
target_type: ImagingVolume
doc: Link to ImagingVolume object from which this data was generated.
- neurodata_type_def: SegmentationLabels
neurodata_type_inc: NWBDataInterface
doc: Segmentation labels
datasets:
- name: labels
dtype: text
dims:
- labels
shape:
- null
doc: ROI labels. Should be the same length as the number of ROIs
- name: description
dtype: text
doc: description of what ROIs represent
links:
- name: ImageSegmentation
target_type: ImageSegmentation
doc: Link to ImageSegmentation object that the labels apply to.
quantity: '?'
- name: MCVSegmentation
target_type: MultiChannelVolume
doc: Link to MultiChannelVolume holding indexed mask of ROIs.
quantity: '?'
- name: MCVSeriesSegmentation
target_type: MultiChannelVolumeSeries
doc: Link to MultiChannelVolumeSeries holding series of indexed masks of ROIs.
quantity: '?'
- neurodata_type_def: PlaneExtension
neurodata_type_inc: PlaneSegmentation
doc: Results from image segmentation of a specific imaging volume