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MIBI Workshop

Tues. August 30th - Thurs. September 1st, 2022
In-person at Stanford University and Online

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Registration link: bit.ly/3vs52Lb
 

Agenda

All times in PDT

Agenda

Tuesday, August 30, 2022

Morning session in BMI 1021

8:00am

8:30am

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9:45am

10:15am

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11:30am

 

12:00pm

 

1:00pm

Opening remarks​

Session I: Building an antibody panel

  • Part 1: Panel construction

  • Part 2: Antibody validation

  • Part 3: When antibodies fail

Break

Session II: Generating a tissue cohort

  • Part 1: Cohort construction and staining

  • Part 2: Cohort acquisition considerations

Ionpath roadmap

     Eric Abel, Ionpath

Lunch

     Edwards courtyard

Panel discussion: Multiplexed imaging project considerations​

     Edwards R358

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Wednesday, August 31, 2022

8:00am

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9:30am

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10:15am

10:45am

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12:00pm

 

1:00pm

Session III: Processing MIBI data

  • Part 1: Rosetta image compensation

  • Part 2: Evaluating Rosetta on your own data

  • Part 3: Quantifying MIBI sensitivity

Machine learning for reference-free alignment and dimension reduction

     Barbara Englehart, Gladstone Institute

Break

Session IV: Pixel-level analysis

  • Part 1: Using pixel clustering to characterize multiplexed imaging data

  • Part 2: Applying pixel clustering to your own data

Lunch

     Edwards courtyard

Computational office hours

     Edwards R141

Morning session in BMI 1021

Thursday, September 1, 2022

Morning session in Alway M112

8:00am

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9:00am

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9:30am

10:00am

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11:45am

12:00pm

 

1:00pm

 

3:00pm

Session V: Cell-level analysis

  • Part 1: Segmentation

  • Part 2: Cell clustering

  • Part 3: Assessing accuracy with Mantis Viewer

A graphical user interface to select FOVs on the MIBIscope

     Marie-Liesse Asselin-Labat & Kenta Yokote, WEHI

Break

Session VI: Spatial analysis

  • Part 1: Choosing the right analysis

  • Part 2: Pairwise distance analysis

  • Part 3: K-means neighborhood analysis

  • Part 4: Spatial LDA neighborhood analysis

Closing remarks

Lunch

     Edwards courtyard

Computational office hours

     Edwards R141

Happy hour!

     Nola, 535 Ramona St, Palo Alto

Zoom links

Zoom links

Morning sessions: Zoom

Afternoon sessions: Zoom (password: 920314)

Pre-recored talks

Pre-recorded talks

Playlist of all videos here

Individual videos:

1. toffy setup

2. MIBI tiling tutorial

3. Image processing and extraction

4. Real-time MIBI monitoring

5. Reorganizing your data

6. Setting up ark

Directions

Directions

291 Campus Drive, Stanford, CA 94043

August 30 and 31 - Biomedical Innovations BMI 1021

September 1 - Alway M112

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