Laboratory Process Automation for Imaging Mass Cytometry

Project Title: Laboratory Process Automation for Imaging Mass Cytometry
Program:
CAREERS (323)

Project Image: https://support.access-ci.org/system/files/webform/project/108/Kakade_Image.jpg
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Status: Halted
Project Leader
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Project Leader:
Vijay Kakade

Email: vijayakumar.kakade@yale.edu
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Mentor(s):
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Project Information
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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 Information Subsection
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Project Deliverables:
Scripts (probably in Python) to automate the operation of Windows software packages. 
Other TBD.

Project Deliverables:
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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:
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Student Facilitator Programming Skill Level: Scripting
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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
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Project Milestones:
- Milestone Title: Startup
  Milestone Description: Meet with project lead to see what is intended. Obtain software documentation. Develop project plan. Give kickoff presentation
  Completion Date Goal: 2020-12-15
- Milestone Title: Intermediate
  Milestone Description: Determine which applications can be automated

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Final Report
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