Laboratory Process Automation for Imaging Mass Cytometry

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

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Status Halted

Project Leader

Project Leader Vijay Kakade

Email vijayakumar.kakade@yale.edu

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Project Information

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

Project Deliverables Scripts (probably in Python) to automate the operation of Windows software packages.
Other TBD.

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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.

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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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