Submission information
Submission Number: 76
Submission ID: 108
Submission UUID: 8eb3c275-2bd8-4a3f-83b4-f96ac8de5820
Submission URI: /form/project
Created: Thu, 11/05/2020 - 11:39
Completed: Thu, 11/05/2020 - 16:41
Changed: Wed, 07/06/2022 - 15:08
Remote IP address: 128.36.7.173
Submitted by: Andrew Sherman
Language: English
Is draft: No
Webform: Project
| Project Title | Laboratory Process Automation for Imaging Mass Cytometry |
|---|---|
| Program | CAREERS |
| Project Image |
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| Tags | |
| Status | Halted |
| Project Leader | Vijay Kakade |
| vijayakumar.kakade@yale.edu | |
| Mobile Phone | |
| Work Phone | |
| Mentor(s) | |
| Student-facilitator(s) | |
| Mentee(s) | |
| Project Description | We are analyzing Imaging Mass Cytometry images (eg., figure attached) using four different software: 1) MCD viewer, 2) Ilastik, 3) cell profiler and 4) Histocat. We have standardized the manual analysis of IMC images. We intend to make this analysis procedure automated, stitching together all four software or possibly into two pieces if Human intervention is required. |
| Project Deliverables | Scripts (probably in Python) to automate the operation of Windows software packages. Other TBD. |
| Project Deliverables | |
| Student Research Computing Facilitator Profile | Undergrad or grad student should be fine, but probably the student needs to understand (or be able to learn independently) how to script applications in a Windows environment. The scripting could be done using Python or other appropriate scripting tools. No specific domain expertise should be required, since that can be provided by the project leader if necessary. |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | Scripting |
| Mentee Programming Skill Level | |
| Project Institution | Yale University |
| Project Address | Connecticut |
| Anchor Institution | CR-Yale |
| Preferred Start Date | 12/01/2020 |
| Start as soon as possible. | No |
| Project Urgency | Already behind3Start date is flexible |
| Expected Project Duration (in months) | |
| Launch Presentation | |
| Launch Presentation Date | |
| Wrap Presentation | |
| Wrap Presentation Date | |
| Project Milestones |
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| Github Contributions | |
| Planned Portal Contributions (if any) | |
| Planned Publications (if any) | |
| What will the student learn? | |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | |
| HPC resources needed to complete this project? | |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | |
| What is the impact on other disciplines? | |
| Is there an impact physical resources that form infrastructure? | |
| Is there an impact on the development of human resources for research computing? | |
| Is there an impact on institutional resources that form infrastructure? | |
| Is there an impact on information resources that form infrastructure? | |
| Is there an impact on technology transfer? | |
| Is there an impact on society beyond science and technology? | |
| Lessons Learned | |
| Overall results |