Finish CV pass, checkin

README.md

@@ -14,82 +14,128 @@ Beth's bio page with contact email
 
 ### CellProfiler
 
-downloads 
+[downloads](https://cellprofiler.org/releases) 
 
-manual 
+[manual](https://broad.io/CellProfilerManual) 
 
-tutorials
+[plugins documentation]()
 
-GitHub 
+[tutorials](https://tutorials.cellprofiler.org/)
+
+[GitHub]()  
 
 [help forum]() 
 
-papers - [2021 (CellProfiler 4)]() [2018 (CellProfiler 3)]()
+[pipeline suggester](https://www.boaq.org)
+
+papers -  [CellProfiler-plugins [2023]](https://doi.org/10.1111/jmi.13223) [CellProfiler 4 [2021](https://doi.org/10.1186/s12859-021-04344-9) [CellProfiler 3 [2018]](https://doi.org/10.1371/journal.pbio.2005970)
 
 ### CellProfiler Analyst
 
-downloads 
+[downloads]()  
 
-manual 
+[manual]()  
 
-GitHub 
+[GitHub]()  
 
 [help forum]() 
 
-papers - 2021 (CellProfiler Analyst 3)
+papers - [2021 (CellProfiler Analyst 3)](https://doi.org/10.1093/bioinformatics/btab634)
 
 ### Piximi
 
-downloads 
+[Piximi.app](https://piximi.app/) 
+
+[manual](https://documentation.piximi.app/)  
+
+[GitHub](https://github.com/piximi/piximi) 
+
+[help forum]() 
 
-manual 
+[preprint](https://doi.org/10.1101/2024.06.03.597232v1)
 
-GitHub 
+### Distributed-Something
 
-help forum 
+[GitHub](https://distributedscience.github.io/Distributed-Something/introduction.html)
 
-preprint
+[paper](https://doi.org/10.1038/s41592-023-01918-8)
 
 ### Bilayers 
 
-demo app
+[demo app]()
 
-GitHub
+[GitHub]()
 
 ## Educational materials
 
-### Papers we wrote
+### Educational papers we wrote
 
-Twenty Questions
+[The Twenty Questions of Bioimage Object Analysis[2023]](https://doi.org/10.1038/s41592-023-01919-7)
 
-Beginner's Guide 
+[A biologist’s guide to planning and performing quantitative bioimaging experiments[2023]](https://doi.org/10.1371/journal.pbio.3002167) 
 
-Common solutions
+[Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions[2024]](https://doi.org/10.1111/jmi.13288)
+
+[A postdoctoral training program in bioimage analysis[2024]](https://doi.org/10.1091/mbc.E24-05-0214)
 
 ### Stuff we make
 
 Lab website
 
 Lab paper pages
 
-[Beth's CV's preprints section](https://docs.google.com/document/d/1zZfoo2b-IbEDbpJ5pH6V0KlfdiY7A-clsAdRr-ouYX8/preview#heading=h.ea9i2felg8yq)
+[Current lab preprints (from Beth's CV)](https://docs.google.com/document/d/1zZfoo2b-IbEDbpJ5pH6V0KlfdiY7A-clsAdRr-ouYX8/preview#heading=h.ea9i2felg8yq)
+
+[Imaging Platform Blog](https://blog.cellprofiler.org)
 
-YouTube tutorials
+YouTube tutorials]()
 
 [Office hours link](broad.io/imagingofficehours)
 
-Forum.image.sc
+The Scientific Community Image Forum - Forum.image.sc]() [paper](https://doi.org/10.1371/journal.pbio.3000340)
+
+[COBA website]()
 
-COBA website
+Bioimaging Guide - [English](https://www.bioimagingguide.org/welcome.html) [Spanish](https://es.bioimagingguide.org/) [Portuguese](https://pt.bioimagingguide.org/) [Czech](https://cs.bioimagingguide.org/) 
 
-Bioimaging Guide - English Spanish Portuguese Czech 
+The Image Based Profiling Handbook]()
 
-The Cell Painting Gallery - [Website] [Paper]
+The Cell Painting Gallery (image repository) - [Website]() [Paper](https://doi.org/10.1038/s41592-024-02399-z)
 
 ### Stuff we contributed to (but others led)
 
-Online guide for checklists for imaging and image analysis
+[Online guide for checklists for imaging and image analysis]() [Paper -  Community-developed checklists for publishing images and image analysis [2023]](https://doi.org/10.1038/s41592-023-01987-9)
+
+Metrics Reloaded online metric chooser]() [Paper 1](https://doi.org/10.1038/s41592-023-02151-z) [Paper 2](https://doi.org/10.1038/s41592-023-02150-0)
+
+Microtutor imaging education platform]()
+
+## Papers you might find useful
+
+### Protocols
+
+[ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis[2020]](https://doi.org/10.1002/cpz1.89)
+
+[Interpreting image-based profiles using Morpheus and single-cell visualization[2023]](https://doi.org/10.1002/cpz1.713)
+
+[Optimizing the Cell Painting assay for image-based profiling[2023]](https://doi.org/10.1038/s41596-023-00840-9)
+
+### Reviews
+
+[Open-source deep-learning software for bioimage segmentation[2021]](https://doi.org/10.1091/mbc.E20-10-0660)
+
+[Defining the boundaries: challenges and advances in identifying cells in microscopy images[2024]](https://doi.org/10.1016/j.copbio.2023.103055)
+
+### Community Surveys
+
+[2020 BioImage Analysis Survey: Community experiences and needs for the future[2021]](https://doi.org/10.1017/S2633903X21000039)
+
+[Bridging Imaging Users to Imaging Analysis - A community survey[2023]](https://doi.org/10.1111/jmi.13229)
+
+### Opinions/Perspectives
+
+[Moving beyond the desktop: Prospects for Practical Bioimage Analysis via the Web[2023]](https://doi.org/10.3389/fbinf.2023.1233748)
 
-Metrics Reloaded metric chooser
+[A Call for FAIR and Open-Access Training Materials to advance Bioimage Analysis[2024]](https://doi.org/10.31219/osf.io/2zgmc)
 
-Microtutor imaging education
+[The Crucial Role of BioImage Analysts in Scientific Research and Publication](https://doi.org/10.5281/zenodo.11457452)