• What they want to measure?
• How precise these measurements must be for drawing meaningful conclusions from their experiments.

There is really no such thing as a ‘one size fits all’ image analysis workflow or software that, in one shot, covers all the requirements for all the interpretations a researcher might hope to glean from a particular image assay.

Instead, the assay design itself, the details of the microscopy imaging, and the target image analysis metrics all have to work together to achieve this goal of biological interpretability.

In this workshop, participants will work closely with members of the Allen Institute for Cell Science to address these questions and identify validated quantitative approaches that can be applied to their own imaging data to appropriately address their underlying biological questions.

This workshop is for individuals who have a well-defined project with clear questions that require quantitative answers, and who also have a dataset that they think is appropriate, but may be missing the computational skills they need to perform rigorous, quantitative data analysis on their imaging data. We are open to any model system and any biological question. Due to the expertise at the Allen Institute for Cell Science, we prefer candidates who use light microscopy (particularly fluorescence microscopy) but may consider individuals with electron microscopy data on a case-by-case basis. While we do not have specific coding requirements, participants with a working knowledge of Python and data storage will be the best prepared to get the most from this workshop.

Who Should Attend?

Candidates who use light microscopy (particularly fluorescence microscopy)

Candidates with a working knowledge of Python and Data Storage

Potential Participant Questions:

1. Describe your biological question.
2. What kind of bright-field or fluorescent images are you acquiring?
3. What problems are you currently encountering? For example: segmentations, tracking, feature extraction, signal to noise ratio, assay design, etc.
4. Are there specific computational tools that you are looking to gain experience with?

Exclusion Criteria:

1. Individuals with absolutely no programming experience (scripting in ImageJ counts as experience!)
2. Individuals without any image data of their own to analyze

In the months prior to the workshop, our team at the Allen Institute will schedule individual 30-60 minute meetings (by Zoom) to better understand the questions and needs of each participant, and potentially suggest some preparation to maximize their time at the workshop.

Cost To Attend: The workshop is free to accepted applicants.

Deadline Date: Friday, March 29, 2024