Hawley Helmbrecht

She/Her | Postdoc Jantzie Lab @HopkinsMedicine | PhD Nance Lab @UWChemE | Applying #datascience 💻 to Quantifying 🧠 #cellmorphology in #neurodevelopment

[Hawley Helmbrecht @HawleyHelm]

I am excited to share that the most recent paper from my Ph.D. with @profnance, "Prevalence and practices of immunofluorescent cell image processing: a systematic review" is now published in Frontiers in Cellular Neuroscience!

Link: https://t.co/hmbfQAPmpr

[Hawley Helmbrecht @HawleyHelm]

@profnance @Tale_of_2_PhDs We also have unlisted videos on tips for resumes and applications and career panels. They are unlisted due to personal information (I don't want my terrible old resumes everywhere on the internet).

But if you are interested, message me for a link!

[Hawley Helmbrecht @HawleyHelm]

For our summer data science training program in @profnance 's lab, we developed professional development workshops for our high school and undergraduate students and made them available on YouTube.

Link to Playlist: https://t.co/6Yzr212M7J

[Hawley Helmbrecht @HawleyHelm]

@profnance @Tale_of_2_PhDs Video 6: A final Instructor panel answering questions from the summer.

Watch for general and specific questions about research!

Stay tuned for tips for making the most of high school and undergrad to support research careers (hint: enjoy life)!

Link: https://t.co/aX2fsjpaYl

[Hawley Helmbrecht @HawleyHelm]

To help people improve image processing and cell quantification of their own images, we also include supplementary tables that list each cell type alongside the models, image processing methods, and feature quantified tagged with the related citation from our literature review.

[Hawley Helmbrecht @HawleyHelm]

I am excited to share that the most recent paper from my Ph.D. with @profnance, "Prevalence and practices of immunofluorescent cell image processing: a systematic review" is now published in Frontiers in Cellular Neuroscience!

Link: https://t.co/hmbfQAPmpr

[Hawley Helmbrecht @HawleyHelm]

We show that less than 10% of the over 9,000 papers published with immunofluorescent images of central nervous system cells include image processing methodologies in the publication.

[Hawley Helmbrecht @HawleyHelm]

Then, we conclude with a Roadmap for Enhancing Cell Quantification with Improved Image Processing (Box 1).

[Hawley Helmbrecht @HawleyHelm]

We created a beautiful Sankey diagram showing the combinations of models, central nervous system cells, quantified features, image processing techniques, and software used for all papers using confocal microscopy (Figure 3).

[Hawley Helmbrecht @HawleyHelm]

We designed multi-level pie charts and tree diagrams to show the prevalence of common fluorescent imaging methods across different cells of the CNS and with different image processing methods (Figure 2).

[Hawley Helmbrecht @HawleyHelm]

We provide a table of the most commonly published image processing software, including their costs, features, and citations for quantifying morphological cell characteristics (Table 1).

[Hawley Helmbrecht @HawleyHelm]

Data Science Module 6: Research Paper-Specific Workflow

Link: https://t.co/67TThpKfhG

I walk students through the workflow for microglial analysis from our 2020 Bioengineering & Translational Medicine paper and output a CSV of over 30,000 cells and their quantified features.

[Hawley Helmbrecht @HawleyHelm]

Our summer learning modules about data science for fluorescent brain cell imaging in the Nance Lab @profnance at @UWChemE are up as a playlist on Youtube:https://t.co/H1JJeiW6wl

The series was developed for high schoolers and undergraduates with no previous research experience.

[Hawley Helmbrecht @HawleyHelm]

Data Science Module 6 - Getting Quantitative Cell Characteristics

Link: https://t.co/Zpn6qz67E7

I teach students how to get quantitative cell features of microglia from images published in Nance Lab research papers.

[Hawley Helmbrecht @HawleyHelm]

Meet the Instructors Panel: https://t.co/ZXaPUGosUR

Introduces students to Phuong Nguyen, Nels Schimek, and me - all graduate students in the Nance Lab. We discuss our paths to neurodevelopmental engineering research, current projects, and teaching goals.

[Hawley Helmbrecht @HawleyHelm]

Data Science Module 4 - The Power of Thresholds

Link: https://t.co/Avg6q1zCZj

I introduce students to the concept of thresholds and apply thresholds to immunofluorescent images of brain cells.

[Hawley Helmbrecht @HawleyHelm]

Machine Learning Module 2 - Unsupervised Machine Learning Applied to Multiple Particle Tracking

Link: https://t.co/goFGl8cISF

Nels Schimek introduces students to unsupervised learning approaches to analyzing multiple particle trajectories in brain slices.

[Hawley Helmbrecht @HawleyHelm]

Machine Learning Module 1 - Multiple Particle Tracking

Link: https://t.co/6QwXKEwHg0

Nels Schimek introduces our students to machine learning applied to multiple particle tracking in brain slices.