From 303d954f33d75349f1b90f8033e99411234a6ef6 Mon Sep 17 00:00:00 2001 From: juhuntenburg Date: Tue, 14 Mar 2023 12:16:45 +0100 Subject: [PATCH 1/3] fix label dstypes --- alyx/data/fixtures/data.datasettype.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/alyx/data/fixtures/data.datasettype.json b/alyx/data/fixtures/data.datasettype.json index 728e9f78..bee7aff1 100644 --- a/alyx/data/fixtures/data.datasettype.json +++ b/alyx/data/fixtures/data.datasettype.json @@ -1764,7 +1764,7 @@ "pk": "479ea451-e7d5-413a-8dc1-e8eb44e5afc2", "fields": { "json": null, - "name": "_ibl_videoTracking.trainingDataPaw", + "name": "videoTracking.trainingDataPaw", "created_by": null, "description": "Manual labels of the paws for training pose estimation algorithms. Contains csv files with labels, frame images and short video snippets from various sessions", "filename_pattern": "" @@ -1775,7 +1775,7 @@ "pk": "4ef9e5ed-c132-4329-a9b0-63260c26ccac", "fields": { "json": null, - "name": "_ibl_videoTracking.trainingDataPupil", + "name": "videoTracking.trainingDataPupil", "created_by": null, "description": "Manual labels of the pupils for training pose estimation algorithms. Contains csv files with labels, frame images and short video snippets from various sessions", "filename_pattern": "" From da678c85283361aaca3cf00df7c940a43085e070 Mon Sep 17 00:00:00 2001 From: juhuntenburg Date: Tue, 14 Mar 2023 13:46:55 +0100 Subject: [PATCH 2/3] lightning pose dataset type --- alyx/data/fixtures/data.datasettype.json | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/alyx/data/fixtures/data.datasettype.json b/alyx/data/fixtures/data.datasettype.json index bee7aff1..c7919ea1 100644 --- a/alyx/data/fixtures/data.datasettype.json +++ b/alyx/data/fixtures/data.datasettype.json @@ -1780,5 +1780,16 @@ "description": "Manual labels of the pupils for training pose estimation algorithms. Contains csv files with labels, frame images and short video snippets from various sessions", "filename_pattern": "" } + }, + { + "model": "data.datasettype", + "pk": "bb1add37-910b-4153-bd50-53dc5c9bf77a", + "fields": { + "json": null, + "name": "camera.lightningPose", + "created_by": null, + "description": "Dataframe with coordinates of body parts as estimated by Lightning Pose algorithm", + "filename_pattern": "" + } } ] From 5c9272ebd7d75da7631df4757b082b2608e62ada Mon Sep 17 00:00:00 2001 From: juhuntenburg Date: Wed, 15 Mar 2023 09:14:20 +0100 Subject: [PATCH 3/3] imaging dataset types --- alyx/data/fixtures/data.datasettype.json | 198 +++++++++++++++++++++++ 1 file changed, 198 insertions(+) diff --git a/alyx/data/fixtures/data.datasettype.json b/alyx/data/fixtures/data.datasettype.json index c7919ea1..a6c7124d 100644 --- a/alyx/data/fixtures/data.datasettype.json +++ b/alyx/data/fixtures/data.datasettype.json @@ -1791,5 +1791,203 @@ "description": "Dataframe with coordinates of body parts as estimated by Lightning Pose algorithm", "filename_pattern": "" } + }, + { + "model": "data.datasettype", + "pk": "533c2ab3-3f44-463d-9a07-770c477d6954", + "fields": { + "json": null, + "name": "mpci.componentsActivity", + "created_by": null, + "description": "SVT of singular value compression, separately for each plane", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "462a0471-ff2e-43d1-a70a-dd13bbab1d88", + "fields": { + "json": null, + "name": "mpci.ROIActivityF", + "created_by": null, + "description": "Mean activity of all pixels in each ROI", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "beee53c8-273a-42d4-b171-750f43db6ac0", + "fields": { + "json": null, + "name": "mpci.ROINeuropilActivityF", + "created_by": null, + "description": "Mean activity neuropil pixels neighboring each ROI", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "bef8f983-d194-458c-aa3b-a23789723da3", + "fields": { + "json": null, + "name": "mpci.ROIActivityDeconvolved", + "created_by": null, + "description": "Neuropil-subtracted deconvolved activity of each ROI using standard parameters", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "d30a5416-8c0f-45d1-b444-daed3cbd14dd", + "fields": { + "json": null, + "name": "mpci.times", + "created_by": null, + "description": "Times of each frame", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "c09943db-a710-4482-8eb0-beabceedeb93", + "fields": { + "json": null, + "name": "mpci.badFrames", + "created_by": null, + "description": "Bad frames as identified by processing software", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "d4cb6475-2863-4ab9-bc89-993bdf84fe01", + "fields": { + "json": null, + "name": "mpci.mpciFrameQC", + "created_by": null, + "description": "Frame-level quality control as added by experimenter. 0 means good, other values defined in mpciFrameQC.names.tsv", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "eddc887f-d9e6-4bb1-86b1-1520e9f1ee54", + "fields": { + "json": null, + "name": "mpciFrameQC.names", + "created_by": null, + "description": "", + "filename_pattern": "Human-readable definition of QC types. 0 always should mean good." + } + }, + { + "model": "data.datasettype", + "pk": "47f99a07-9244-4c8d-8851-733f23df9393", + "fields": { + "json": null, + "name": "mpciComponents.images", + "created_by": null, + "description": "Component image for each plane", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "3759b20a-d83b-43c1-b4d7-abf91406433f", + "fields": { + "json": null, + "name": "mpciMeanImage.images", + "created_by": null, + "description": "Mean image for each plane and each channel. Channel 0 should be the calcium-sensitive channel", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "3777d0d9-ea37-489b-be6e-73e7fc6ff36a", + "fields": { + "json": null, + "name": "mpciROIs.stackPos", + "created_by": null, + "description": "X, Y, and Z (plane) coordinate of each ROI's centroid", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "8103033c-f8a6-482a-9ca3-e932c8d2f9af", + "fields": { + "json": null, + "name": "mpciROIs.mlapdv", + "created_by": null, + "description": "Allen CCF coordinates of each ROI centroid", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "96b0c2af-86ce-4a20-9ffa-06e90f900069", + "fields": { + "json": null, + "name": "mpciROIs.mpciROITypes", + "created_by": null, + "description": "Numerical code of ROI type for each ROI", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "a0d580cb-bf14-448b-872a-4a5023e4ce24", + "fields": { + "json": null, + "name": "mpciROIs.masks", + "created_by": null, + "description": "Floating-point mask of each ROI, in 2d or 3d according to how you did detection. Saved as sparse array", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "4871a117-728c-4cc1-b64d-f82d29f81f8b", + "fields": { + "json": null, + "name": "mpciROIs.neuropilMasks", + "created_by": null, + "description": "Floating-point neuropil mask for each ROI, in 2d or 3d according to how you did detection. Saved as a sparse array", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "606674e5-adfa-4049-9f2b-03a1b40c9099", + "fields": { + "json": null, + "name": "mpciROITypes.names", + "created_by": null, + "description": "String describing each ROI type", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "d0236da1-008c-458d-ab8d-c74d22c76148", + "fields": { + "json": null, + "name": "mpciROIs.cellClassifier", + "created_by": null, + "description": "Floating-point cell classifier score for each ROI, ranging between 0 and 1", + "filename_pattern": "" + } + }, + { + "model": "data.datasettype", + "pk": "ccc2bc98-e708-44f4-a6fe-4eabe6766ece", + "fields": { + "json": null, + "name": "mpciStack.timeshift", + "created_by": null, + "description": "Offset time for scanning of each voxel in the stack", + "filename_pattern": "" + } } ]