WayScience · gwaybio · Mar 4, 2025 · Mar 4, 2025 · Mar 4, 2025 · Mar 4, 2025
diff --git a/.github/workflows/auto-cite.yaml b/.github/workflows/auto-cite.yaml
@@ -20,7 +20,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.7
+          python-version: 3.12
       - name: Install Manubot
         run: pip install --upgrade manubot
       - name: Build updated citations

diff --git a/_data/citations.yaml b/_data/citations.yaml
@@ -1,15 +1,148 @@
 # GENERATED AUTOMATICALLY, DO NOT EDIT
 
-- id: 10.1101/2024.03.13.584858
-  title: Toward generalizable phenotype prediction from single-cell morphology representations
+- id: 10.1038/s41592-025-02611-8
+  title: Reproducible image-based profiling with Pycytominer
   authors:
+  - Erik Serrano
+  - Srinivas Niranj Chandrasekaran
+  - Dave Bunten
+  - Kenneth I. Brewer
   - Jenna Tomkinson
   - Roshan Kern
+  - Michael Bornholdt
+  - Stephen J. Fleming
+  - Ruifan Pei
+  - John Arevalo
+  - Hillary Tsang
+  - Vincent Rubinetti
+  - Callum Tromans-Coia
+  - Tim Becker
+  - Erin Weisbart
+  - Charlotte Bunne
+  - Alexandr A. Kalinin
+  - Rebecca Senft
+  - Stephen J. Taylor
+  - Nasim Jamali
+  - Adeniyi Adeboye
+  - Hamdah Shafqat Abbasi
+  - Allen Goodman
+  - Juan C. Caicedo
+  - Anne E. Carpenter
+  - Beth A. Cimini
+  - Shantanu Singh
+  - Gregory P. Way
+  publisher: Nature Methods
+  date: '2025-03-03'
+  link: https://doi.org/g863nc
+  image: https://raw.githubusercontent.com/cytomining/pycytominer/master/logo/just-icon.png
+  tags:
+  - image-based profiling
+  - bioinformatics
+  - software
+  - cell morphology
+  extra-links:
+  - type: software
+    link: https://github.com/cytomining/pycytominer
+    text: GitHub
+- id: 10.1101/2024.09.11.612546
+  title: High-content microscopy and machine learning characterize a cell morphology
+    signature of<i>NF1</i>genotype in Schwann cells
+  authors:
+  - Jenna Tomkinson
   - Cameron Mattson
+  - Michelle Mattson-Hoss
+  - Herb Sarnoff
+  - Stephanie J. Bouley
+  - James A. Walker
+  - Gregory P. Way
+  publisher: Cold Spring Harbor Laboratory
+  date: '2024-09-16'
+  link: https://doi.org/g863nd
+  image: https://www.biorxiv.org/content/biorxiv/early/2024/09/16/2024.09.11.612546/F1.large.jpg
+  tags:
+  - image-based profiling
+  - neurofibromatosis type 1
+  - cell morphology
+  - assay development
+  extra-links:
+  - type: software
+    link: https://github.com/WayScience/nf1_schwann_cell_morphology_signature
+    text: Analysis code
+  - type: software
+    link: https://github.com/WayScience/nf1_schwann_cell_painting_data
+    text: Data processing code
+- id: 10.1038/s41592-024-02537-7
+  title: A genome-wide atlas of human cell morphology
+  authors:
+  - Meraj Ramezani
+  - Erin Weisbart
+  - Julia Bauman
+  - Avtar Singh
+  - John Yong
+  - Maria Lozada
+  - Gregory P. Way
+  - Sanam L. Kavari
+  - Celeste Diaz
+  - Eddy Leardini
+  - Gunjan Jetley
+  - Jenlu Pagnotta
+  - Marzieh Haghighi
+  - Thiago M. Batista
+  - "Joaqu\xEDn P\xE9rez-Schindler"
+  - Melina Claussnitzer
+  - Shantanu Singh
+  - Beth A. Cimini
+  - Paul C. Blainey
+  - Anne E. Carpenter
+  - Calvin H. Jan
+  - James T. Neal
+  publisher: Nature Methods
+  date: '2025-01-27'
+  link: https://doi.org/g826g9
+  image: https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41592-024-02537-7/MediaObjects/41592_2024_2537_Fig1_HTML.png
+  tags:
+  - image-based profiling
+  - pooled cell painting
+  - cell morphology
+  extra-links:
+  - type: source
+    link: https://github.com/broadinstitute/pooled-cell-painting-image-processing
+    text: GitHub
+- id: 10.1101/2024.11.16.623947
+  title: Combining NeuroPainting with transcriptomics reveals cell-type-specific morphological
+    and molecular signatures of the 22q11.2 deletion
+  authors:
+  - Matthew Tegtmeyer
+  - Dhara Liyanage
+  - Yu Han
+  - Kathryn B. Hebert
+  - Ruifan Pei
   - Gregory P. Way
+  - Pearl V. Ryder
+  - Derek Hawes
+  - Callum Tromans-Coia
+  - Beth A. Cimini
+  - Anne E. Carpenter
+  - Shantanu Singh
+  - Ralda Nehme
   publisher: Cold Spring Harbor Laboratory
-  date: '2024-03-13'
-  link: https://doi.org/gtrgrh
+  date: '2024-11-17'
+  link: https://doi.org/g863nf
+  image: https://www.biorxiv.org/content/biorxiv/early/2024/11/17/2024.11.16.623947/F1.large.jpg
+  tags:
+  - image-based profiling
+  - cell painting
+  - data integration
+- id: 10.1186/s44330-024-00014-3
+  title: Toward generalizable phenotype prediction from single-cell morphology representations
+  authors:
+  - Jenna Tomkinson
+  - Roshan Kern
+  - Cameron Mattson
+  - Gregory P. Way
+  publisher: BMC Methods
+  date: '2024-12-09'
+  link: https://doi.org/g863ng
   image: https://github.com/WayScience/phenotypic_profiling/blob/main/7.figures/figures/figure1_panelB.png?raw=true
   tags:
   - single-cell

diff --git a/_data/sources.yaml b/_data/sources.yaml
@@ -1,4 +1,50 @@
-- id: 10.1101/2024.03.13.584858 
+- id: 10.1038/s41592-025-02611-8
+  image: https://raw.githubusercontent.com/cytomining/pycytominer/master/logo/just-icon.png
+  tags:
+    - image-based profiling
+    - bioinformatics
+    - software
+    - cell morphology
+  extra-links:
+    - type: software
+      link: https://github.com/cytomining/pycytominer
+      text: GitHub
+
+- id: 10.1101/2024.09.11.612546 
+  image: https://www.biorxiv.org/content/biorxiv/early/2024/09/16/2024.09.11.612546/F1.large.jpg
+  tags:
+    - image-based profiling
+    - neurofibromatosis type 1
+    - cell morphology
+    - assay development
+  extra-links:
+    - type: software
+      link: https://github.com/WayScience/nf1_schwann_cell_morphology_signature
+      text: Analysis code
+    - type: software
+      link: https://github.com/WayScience/nf1_schwann_cell_painting_data
+      text: Data processing code
+
+
+- id: 10.1038/s41592-024-02537-7
+  image: https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41592-024-02537-7/MediaObjects/41592_2024_2537_Fig1_HTML.png
+  tags:
+    - image-based profiling
+    - pooled cell painting
+    - cell morphology
+  extra-links:
+    - type: source
+      link: https://github.com/broadinstitute/pooled-cell-painting-image-processing
+      text: GitHub
+
+- id: 10.1101/2024.11.16.623947
+  image: https://www.biorxiv.org/content/biorxiv/early/2024/11/17/2024.11.16.623947/F1.large.jpg
+  tags:
+    - image-based profiling
+    - cell painting
+    - data integration
+
+- id: 10.1186/s44330-024-00014-3
   image: https://github.com/WayScience/phenotypic_profiling/blob/main/7.figures/figures/figure1_panelB.png?raw=true
   tags:
     - single-cell

diff --git a/_data/tools.yaml b/_data/tools.yaml
@@ -12,12 +12,19 @@
   description: Python package for enabling single-cell microscopy analysis
   repo: cytomining/cytotable
 
-- name: CytoSnake
+- name: coSMicQC
   group: featured
-  image: https://raw.githubusercontent.com/wayscience/cytosnake/master/logo/just-icon.png
-  link: https://github.com/wayscience/cytosnake
-  description: Python package for orchestrating customized image-based profiling pipelines
-  repo: wayscience/cytosnake
+  image: https://raw.githubusercontent.com/wayscience/coSMicQC/main/media/logo/just-icon.png
+  link: https://github.com/WayScience/coSMicQC
+  description: Python package for single-cell quality control
+  repo: wayscience/cosmicqc
+
+#- name: CytoSnake
+#  group: featured
+#  image: https://raw.githubusercontent.com/wayscience/cytosnake/master/logo/just-icon.png
+#  link: https://github.com/wayscience/cytosnake
+#  description: Python package for orchestrating customized image-based profiling pipelines
+# repo: wayscience/cytosnake
 
 - name: BioBombe
   group: more

diff --git a/_includes/gallery.html b/_includes/gallery.html
@@ -9,8 +9,7 @@
 {%- endfor -%}
 
 <div class="gallery" data-style="{{ include.style }}" data-number="{{ max }}">
-  {%- for i in (1..100) -%}
-
+  {%- for i in (1..max) -%}
     {%- assign image = "image" | append: i -%}
     {%- assign image = include[image] -%}
     {%- assign tooltip = "tooltip" | append: i -%}
@@ -20,13 +19,18 @@
 
     {%- if image -%}
       <a
-        {% if link %}href="{{ link | relative_url }}"{% endif %}
+        {% if link %}
+          {% if link contains "http" %}
+            href="{{ link }}"
+          {% else %}
+            href="{{ link | relative_url }}"
+          {% endif %}
+        {% endif %}
         class="gallery_item"
-        data-tooltip="{{ tooltip }}"
+        {% if tooltip %}data-tooltip="{{ tooltip }}"{% endif %}
       >
         <img src="{{ image | relative_url }}" loading="lazy">
       </a>
     {%- endif -%}
-
   {%- endfor -%}
-</div>
+</div>
diff --git a/_members/cameron-mattson.md b/_members/cameron-mattson.md
@@ -12,6 +12,7 @@ aliases:
 links:
   email: [email protected]
   github: https://github.com/MattsonCam
+group: active
 ---
 
 Cameron graduated with his B.S. in Bioengineering at the University of Colorado, where he implemented and developed physiological models.

diff --git a/_members/dave-bunten.md b/_members/dave-bunten.md
@@ -13,6 +13,7 @@ links:
   orcid: 0000-0001-6041-3665
   email: [email protected]
   github: d33bs
+group: active
 ---
 
 Dave Bunten is a software developer with a passion for expanding human potential through software design, collaboration, and innovation.

diff --git a/_members/erik-serrano.md b/_members/erik-serrano.md
@@ -15,6 +15,7 @@ links:
   email: [email protected]
   github: axiomcura
   twitter: axiomcura
+group: active
 ---
 
 Erik Serrano is a Computational Bioscience (CPBS) PhD student at the Univeristy of Colorado, Anschutz Medical Campus (CU-AMC).

diff --git a/_members/gregory-way.md b/_members/gregory-way.md
@@ -18,7 +18,7 @@ links:
   email: [email protected]
   github: gwaybio
   twitter: gwaybio
-  google-scholar:: iDKZaA4AAAAJ
+  google-scholar: iDKZaA4AAAAJ
 ---
 
 

diff --git a/_members/jacey-curd.md b/_members/jacey-curd.md
@@ -12,6 +12,7 @@ aliases:
 links:
   email: [email protected]
   github: JaceyBronte
+group: active
 ---
 
 Jacey graduated with B.S. degrees in Computer Science and Biology from Duke University, where she worked in Dr. Raluca Gordan’s lab on CRISPR and MutS.

diff --git a/_members/jenna-tomkinson.md b/_members/jenna-tomkinson.md
@@ -12,6 +12,7 @@ links:
   orcid: 0000-0003-2676-5813
   email: [email protected]
   github: jenna-tomkinson
+group: active
 ---
 
 Jenna is a Quantitative Cell Biologist at the Way Lab.

diff --git a/_members/mike-lippincott.md b/_members/mike-lippincott.md
@@ -15,6 +15,7 @@ links:
   email: [email protected]
   github: MikeLippincott
   twitter: mike_lippincott
+group: active
 ---
 
 Mike Lippincott is a Cell Biology, Stem Cells, and Development (CSD) PhD student at the University of Colorado, Anschutz Medical Campus.

diff --git a/_members/roshan-kern.md b/_members/roshan-kern.md
@@ -12,12 +12,14 @@ links:
   orcid: 0000-0002-5605-4759
   email: [email protected]
   github: roshankern
+group: alum
 ---
 
-Roshan is a summer intern at the Way Lab.
+Roshan was a summer intern at the Way Lab.
 He is an undergraduate student at [Case Western Reserve University](https://case.edu/) majoring in systems biology.
-He is currently focused on the analysis of nuclei morphology features for a generalizable cell cycle model.
-He is a major proponent of workflows that are easy to access, interpret, and reproduce.
+In the Way Lab, he focused on the analysis of nuclei morphology features for a generalizable cell cycle model.
+He published papers related to predicting phenotypes from nuclei images and contributed to the pycytominer software package.
+He made several other important contributions to the lab, as it was just getting off the ground.
 
 Roshan is a native of the Denver area and enjoys spending time outside hiking or playing a sport.
 His other interests include spending time with friends, working out, and watching YouTube.
diff --git a/images/funding/NHLBI_logo.png b/images/funding/NHLBI_logo.png
diff --git a/images/funding/aha_logo.jpg b/images/funding/aha_logo.jpg
diff --git a/images/funding/alsf_logo.png b/images/funding/alsf_logo.png
diff --git a/images/funding/amed_logo.jpg b/images/funding/amed_logo.jpg
diff --git a/images/funding/gff_logo.jpg b/images/funding/gff_logo.jpg
diff --git a/index.md b/index.md
@@ -4,11 +4,11 @@ title: Home
 
 Welcome to the Way Lab at [The University of Colorado Anschutz](https://www.cuanschutz.edu/)!
 
-The mission of our lab is to reduce human suffering by integrating biomedical data science and software engineering into drug discovery and translational research.
-We develop new computational methods, innovative approaches, assays, and software for analyzing high-dimensional genomic, molecular, and microscopy data.
-We focus on pediatric diseases, including pediatric cancer and Neurofibromatosis Type 1 (NF1).
+The mission of our lab is to reduce human suffering.
+We develop new computational methods and software for analyzing microscopy images of cells.
+With our collaborators around the world, we develop innovative assays and approaches for making sense of high-content microscopy.
+We focus on pediatric diseases, including pediatric cancer and Neurofibromatosis Type 1 (NF1), and we also have applications in discovering new treatments for cardiac fibrosis.
 
-We perform team science with multidisciplinary collaborators to amplify the impact of our computationally-focused work.
 We also perform open science, making all of our work immediately open for anyone to use and build upon.
 
 {%
@@ -37,7 +37,7 @@ We also perform open science, making all of our work immediately open for anyone
 # Highlights
 
 {% capture text %}
-We develop computational methods and innovative approaches to find better drugs for pediatric diseases.
+We develop computational methods and innovative approaches to analyze high-content microscopy images of cells.
 
 [Research focus and publications &nbsp;→](research)
 {:.center}
@@ -52,7 +52,7 @@ We develop computational methods and innovative approaches to find better drugs
 %}
 
 {% capture text %}
-We release public data and open source software to enable reproducible computational biology analyses and workflows.
+We release public data and open source software and methods to enable reproducible analysis of microscopy images.
 
 [Software &nbsp;→](software)
 {:.center}