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Generalized Workflow
- GeneralWorkflow.pdf: Generalized workflow for mouse BIRN
- Workflow_Expt.pdf: Experimental setup: diagram with questions and answers
- Workflows_prep.pdf: Preparation: diagram with questions and answers
- Workflows_data_col.pdf: Data collection: diagram with questions and answers
- Workflows_data_pro.pdf: Data Processing: diagram with questions and answers
Minutes from meetings
- mouseworkflowsminutes05_05_06.doc: Minutes from first VTC, 05/05/06
- Workflows from the Mouse BIRN AHM can be found here
Duke CIVM MR Imaging and Analysis Workflow
| Stage | Action | Data |
|---|---|---|
| Model Definition | Internal External Investigator defines model of interest and biomarker. Concept definition. | Project summary & Contact Info |
| CIVM project proposal | Investigator defines scientific goal, need for resources | -Project code -Local Investigator -External Collaborator related information -Nature of collaboration -Funding source |
| IACUC | Investigator defines -strain -no of animals -source -animal handling & procedures & drugs to be administered -imaging procedures -expected outcome | -Animal population information -Research Plan |
| Animal Preparation & Perfusion | Duke technician enters: -animal information: ID, age, sex, weight, date of arrival -appropriate metada-, perfusion details, drugs administered -These data go into the animal database | -Specific/Individual animal info -Animal preparation methods -Observations/Notes |
| Scan | -Standard coil, specimen position, image sequence, scan parameters -Duke investigator enters location in DUKE database where data needs to be archived, project code, animal ID -Image metadata extracted automatically from scan header and used in the recon and archiving steps. | -Scan parameters -Raw data |
| Reconstruction | Reconstruction of raw data to image | Image and reconstruction parameters |
| Archive Original Scans | Image data are stored together with animal data -quick view of image data from database html interface -Image and animal database are connected so one can query either | -Results of queries to either image or animal database -Directory structure |
| Post Process | T2 weighted image calculation, alignment to reference target | Derived image set (T2W) |
| Segmentation & Atlasing | Segmentation pipeline: incorporates skull stripping, registration, intensity normalization. (for details: Neuroimage. 2005 Aug 15;27(2):425-35. ) | Bit maps of segmented volumes, registration transforms |
| Morphometric analysis | Registration, surface generation, global and local shape analysis (for details Badea. A, in preparation) | Volume, area, shape info, variability info |
- the T2 image calculation pipeline is complete
- the segmentation pipeline integrating Anjum's thesis work is complete, and includes extensions for new priors
- putting specimens, segmentation and atlases in Paxinos coordinates and orientation, in progress.
- registering with 3D Paxinos atlas contours or histology reconstruction if these exist, in progress
See this page for the working page for simple data sharing between CIT and UCLA
- EAEexample.doc: Example of simple data sharing between CIT and UCLA + potential questions
- EAE3metadata.xls: metadata from Allan for the EAE workflow
Attachment  | Action | Size | Date | Who | Comment |
|---|---|---|---|---|---|
 GeneralWorkflow.pdf | manage | 132.5 K | 09 May 2006 - 19:41 | JylBoline | Generalized workflow for mouse BIRN |
 mouseworkflowsminutes05_05_06.doc | manage | 35.5 K | 09 May 2006 - 23:33 | JylBoline | Minutes from first VTC, 05/05/06 |
| EAEexample.doc | manage | 33.0 K | 28 Aug 2006 - 23:43 | JylBoline | Example of simple data sharing between CIT and UCLA + potential questions |
| Workflow_Expt.pdf | manage | 25.0 K | 03 Oct 2006 - 23:39 | JylBoline | Experimental setup: diagram with questions and answers |
| Workflows_prep.pdf | manage | 19.0 K | 03 Oct 2006 - 23:40 | JylBoline | Preparation: diagram with questions and answers |
| Workflows_data_col.pdf | manage | 18.3 K | 03 Oct 2006 - 23:40 | JylBoline | Data collection: diagram with questions and answers |
| Workflows_data_pro.pdf | manage | 22.5 K | 03 Oct 2006 - 23:42 | JylBoline | Data Processing: diagram with questions and answers |
 EAE3metadata.xls | manage | 46.0 K | 23 Jan 2007 - 19:58 | JylBoline | metadata from Allan for the EAE workflow |
| EAE_work_data_flow.doc | manage | 56.0 K | 24 Jan 2007 - 20:43 | EdrissMerchant | Helps to document the work flow and data flow of EAE collaboration between UCLA and Caltech. |
| EAE_work_data_flow_caltech.doc | manage | 55.5 K | 08 Feb 2007 - 16:20 | EdrissMerchant | Documents the work and data flow for the EAE collaboration between UCLA and Caltech. This is from Caltech's perspective. |