From eb3e614d08236b2f4c94849db1485ca71ef39805 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Mon, 13 Jun 2022 13:21:27 -0400 Subject: [PATCH 1/9] Update nwb.ophys.yaml --- core/nwb.ophys.yaml | 93 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) diff --git a/core/nwb.ophys.yaml b/core/nwb.ophys.yaml index ab049e73..d593f1f7 100644 --- a/core/nwb.ophys.yaml +++ b/core/nwb.ophys.yaml @@ -1,4 +1,97 @@ groups: +- neurodata_type_def: ObjectiveLens + neurodata_type_inc: Device + doc: Metadata about an objective lens data acquisition device for one-photon optical imaging. + attributes: + - name: magnification + dtype: float32 + doc: TODO + required: true + - name: numerical_aperture + dtype: float32 + doc: TODO + required: true + - name: description + dtype: text + doc: Description of the device (e.g., model, firmware version, processing software version, etc.) + as free-form text. + required: false + - name: manufacturer + dtype: text + doc: The name of the manufacturer of the device. + required: false + +- neurodata_type_def: OnePhotonCamera + neurodata_type_inc: Device + doc: Metadata about the camera used as the data acquisition device for one-photon optical imaging. + attributes: + - name: quantum_efficiency + dtype: float32 + doc: TODO + required: false + - name: read_noise + dtype: float32 + doc: Number of electrons. TODO + required: false + - name: description + dtype: text + doc: Description of the device (e.g., model, firmware version, processing software version, etc.) + as free-form text. + required: false + - name: manufacturer + dtype: text + doc: The name of the manufacturer of the device. + required: false + +- neurodata_type_def: OnePhotonSeries + neurodata_type_inc: ImageSeries + doc: Image stack recorded over time from 1-photon microscope. + attributes: + - name: pmt_gain + dtype: float32 + doc: Photomultiplier gain. + required: false + - name: scan_line_rate + dtype: float32 + doc: Lines imaged per second. This is also stored in /general/optophysiology but + is kept here as it is useful information for analysis, and so good to be stored + w/ the actual data. + required: false + - name: exposure_time + dtype: float32 + doc: TODO + required: false + - name: binning + dtype: float32 + doc: TODO + required: false + - name: power + dtype: float32 + doc: TODO + required: false + - name: intensity + dtype: float32 + doc: TODO + required: false + datasets: + - name: field_of_view + dtype: float32 + dims: + - - width|height + - - width|height|depth + shape: + - - 2 + - - 3 + doc: Width, height and depth of image, or imaged area, in meters. + quantity: '?' + links: + - name: objective_lens + target_type: ObjectiveLens + doc: Link to camera device object from which this TimeSeries data was generated. + - name: camera + target_type: OnePhotonCamera + doc: Link to camera device object from which this TimeSeries data was generated. + - neurodata_type_def: TwoPhotonSeries neurodata_type_inc: ImageSeries doc: Image stack recorded over time from 2-photon microscope. From 85f531cb47eeb0596fb526239bc88c6ba7cd67a6 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Mon, 13 Jun 2022 17:44:03 -0400 Subject: [PATCH 2/9] Update nwb.ophys.yaml --- core/nwb.ophys.yaml | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/core/nwb.ophys.yaml b/core/nwb.ophys.yaml index d593f1f7..94ec539f 100644 --- a/core/nwb.ophys.yaml +++ b/core/nwb.ophys.yaml @@ -11,15 +11,6 @@ groups: dtype: float32 doc: TODO required: true - - name: description - dtype: text - doc: Description of the device (e.g., model, firmware version, processing software version, etc.) - as free-form text. - required: false - - name: manufacturer - dtype: text - doc: The name of the manufacturer of the device. - required: false - neurodata_type_def: OnePhotonCamera neurodata_type_inc: Device @@ -33,15 +24,6 @@ groups: dtype: float32 doc: Number of electrons. TODO required: false - - name: description - dtype: text - doc: Description of the device (e.g., model, firmware version, processing software version, etc.) - as free-form text. - required: false - - name: manufacturer - dtype: text - doc: The name of the manufacturer of the device. - required: false - neurodata_type_def: OnePhotonSeries neurodata_type_inc: ImageSeries From 8abafcdc0000446b6abe6fadc5a12cee3626a56c Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Thu, 7 Jul 2022 11:27:02 -0400 Subject: [PATCH 3/9] simplify device metadata --- core/nwb.ophys.yaml | 45 ++++++++------------------------------------- 1 file changed, 8 insertions(+), 37 deletions(-) diff --git a/core/nwb.ophys.yaml b/core/nwb.ophys.yaml index 94ec539f..735e25e4 100644 --- a/core/nwb.ophys.yaml +++ b/core/nwb.ophys.yaml @@ -1,30 +1,4 @@ groups: -- neurodata_type_def: ObjectiveLens - neurodata_type_inc: Device - doc: Metadata about an objective lens data acquisition device for one-photon optical imaging. - attributes: - - name: magnification - dtype: float32 - doc: TODO - required: true - - name: numerical_aperture - dtype: float32 - doc: TODO - required: true - -- neurodata_type_def: OnePhotonCamera - neurodata_type_inc: Device - doc: Metadata about the camera used as the data acquisition device for one-photon optical imaging. - attributes: - - name: quantum_efficiency - dtype: float32 - doc: TODO - required: false - - name: read_noise - dtype: float32 - doc: Number of electrons. TODO - required: false - - neurodata_type_def: OnePhotonSeries neurodata_type_inc: ImageSeries doc: Image stack recorded over time from 1-photon microscope. @@ -41,19 +15,19 @@ groups: required: false - name: exposure_time dtype: float32 - doc: TODO + doc: Exposure time of the sample; often the inverse of the frequency. required: false - name: binning - dtype: float32 - doc: TODO + dtype: uint8 + doc: Amount of pixels combined into 'bins'; could be 1, 2, 4, 8, etc. required: false - name: power dtype: float32 - doc: TODO + doc: Power of the excitation in mW, if known. required: false - name: intensity dtype: float32 - doc: TODO + doc: Intensity of the excitation in mW/mm^2, if known. required: false datasets: - name: field_of_view @@ -67,12 +41,9 @@ groups: doc: Width, height and depth of image, or imaged area, in meters. quantity: '?' links: - - name: objective_lens - target_type: ObjectiveLens - doc: Link to camera device object from which this TimeSeries data was generated. - - name: camera - target_type: OnePhotonCamera - doc: Link to camera device object from which this TimeSeries data was generated. + - name: imaging_plane + target_type: ImagingPlane + doc: Link to ImagingPlane object from which this TimeSeries data was generated. - neurodata_type_def: TwoPhotonSeries neurodata_type_inc: ImageSeries From 82dddeebb073b5a23582fef35d62567deadb5d8c Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Tue, 19 Jul 2022 11:48:48 -0400 Subject: [PATCH 4/9] Update nwb.namespace.yaml --- core/nwb.namespace.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/nwb.namespace.yaml b/core/nwb.namespace.yaml index 06618b81..d2c39c1b 100644 --- a/core/nwb.namespace.yaml +++ b/core/nwb.namespace.yaml @@ -57,4 +57,4 @@ namespaces: - doc: This source module contains neurodata_type for retinotopy data. source: nwb.retinotopy.yaml title: Retinotopy - version: "2.5.0" + version: "2.6.0-alpha" From cd7cb9009315e96eb82e93a5214467fa6eba4904 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Tue, 19 Jul 2022 11:49:46 -0400 Subject: [PATCH 5/9] Update format_release_notes.rst --- docs/format/source/format_release_notes.rst | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst index dd11b616..366c0cd5 100644 --- a/docs/format/source/format_release_notes.rst +++ b/docs/format/source/format_release_notes.rst @@ -3,6 +3,15 @@ Release Notes ============= + +2.6.0-alpha (Upcoming) +---------------------- + +Major changes +^^^^^^^^^^^^^ +- Added OnePhotonSeries. (#523) + + 2.5.0 (June 14, 2022) --------------------- From 9652421189b96aa6fc907d044bd37d48cec4ae37 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Tue, 19 Jul 2022 11:50:55 -0400 Subject: [PATCH 6/9] Update conf.py --- docs/format/source/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/format/source/conf.py b/docs/format/source/conf.py index 2f9ac477..655d13ce 100644 --- a/docs/format/source/conf.py +++ b/docs/format/source/conf.py @@ -83,9 +83,9 @@ def setup(app): # built documents. # # The short X.Y version. -version = '2.5.0' +version = '2.6.0' # The full version, including alpha/beta/rc tags. -release = '2.5.0' +release = '2.6.0-alpha' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. From a4e25bb508e54ec04365cd41d163a45a24c3144d Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Wed, 20 Jul 2022 11:32:41 -0400 Subject: [PATCH 7/9] add unit to FoV --- core/nwb.ophys.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/core/nwb.ophys.yaml b/core/nwb.ophys.yaml index 735e25e4..f190283f 100644 --- a/core/nwb.ophys.yaml +++ b/core/nwb.ophys.yaml @@ -38,8 +38,13 @@ groups: shape: - - 2 - - 3 - doc: Width, height and depth of image, or imaged area, in meters. + doc: Width, height and depth of image or imaged area, in meters. quantity: '?' + attributes: + - name: unit + dtype: text + value: meters + doc: Unit of measurement for the width, height, and depth of the image or imaged area. links: - name: imaging_plane target_type: ImagingPlane From 503a57b5f662dea24956211ab9bcab8d741afd07 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Tue, 20 Sep 2022 12:34:59 -0400 Subject: [PATCH 8/9] remove field of view --- core/nwb.ophys.yaml | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/core/nwb.ophys.yaml b/core/nwb.ophys.yaml index f190283f..e5a21bd0 100644 --- a/core/nwb.ophys.yaml +++ b/core/nwb.ophys.yaml @@ -29,22 +29,6 @@ groups: dtype: float32 doc: Intensity of the excitation in mW/mm^2, if known. required: false - datasets: - - name: field_of_view - dtype: float32 - dims: - - - width|height - - - width|height|depth - shape: - - - 2 - - - 3 - doc: Width, height and depth of image or imaged area, in meters. - quantity: '?' - attributes: - - name: unit - dtype: text - value: meters - doc: Unit of measurement for the width, height, and depth of the image or imaged area. links: - name: imaging_plane target_type: ImagingPlane From b91a638a947f9d3a83ed44f01fbf862030c79653 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Wed, 5 Oct 2022 14:48:20 -0400 Subject: [PATCH 9/9] Update format_release_notes.rst --- docs/format/source/format_release_notes.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst index 3f212a58..90842496 100644 --- a/docs/format/source/format_release_notes.rst +++ b/docs/format/source/format_release_notes.rst @@ -7,7 +7,7 @@ Release Notes 2.6.0-alpha (Upcoming) ---------------------- -Major changes +Minor changes ^^^^^^^^^^^^^ - Added OnePhotonSeries. (#523) - ``Subject.age`` has a new optional attribute, ``reference``, which can take a value of "birth" (default) or "gestational". (#525)