A few small resources from Issue #7 (#58)

Author: bethac07

02_Sample_acquisition/Practical_considerations.md

@@ -1,5 +1,7 @@
 # Practical considerations
 
+We recommend checking out [Microtutor](https://microtutor.globalbioimaging.org/) and [MyScope](https://myscope.training/) for interactive explanations of many of these concepts!
+
 ## Objective selection
 
 Microscope objectives have a number of features that must be considered when deciding which objective is right for your experiment

02_Sample_acquisition/Resources.md

@@ -10,6 +10,15 @@
 * - 🌐 Nikon MicroscopyU 
   - [link](https://www.microscopyu.com/microscopy-basics)
   - Fundamentals of microscopy explained for beginners with lots of images and plain language descriptions of terms used in microscopy
+* - 🌐 Microtutor
+  - [link](https://microtutor.globalbioimaging.org/)
+  - A fantastic interactive course on fluorescence microscopy, created by the team at [Harvard CITE](https://cite.hms.harvard.edu/)
+* - 🌐 MyScope
+  - [link](https://myscope.training/)
+  - An interactive microscope simulator and learning environment developed by MicroscopyAustralia, covering a number of types of microscopy.
+* - 📖 Visualizing Cells Through Microscopy
+  - [link](https://open.oregonstate.education/cellbiology/chapter/microscopy/)
+  - An open textbook chapter from the "Fundamentals of Cell Biology" book from Oregon State University, a great introductory guide to concepts in microscopy.
 * - 📄 Seeing is believing? A beginners' guide to practical pitfalls in image acquisition {cite}`North2006-sb`
   - [link](https://doi.org/10.1083/jcb.200507103)
   - An overview of common concerns to check for during sample preparation and image acquisition
@@ -21,7 +30,10 @@
   - Step-by-step guidance on practical considerations for sample preparation, acquisition, and image analysis; primarily though not exclusively aimed at users of confocal microscopy
 * - 📄 Best practices and tools for reporting reproducible fluorescence microscopy methods {cite}`Montero_Llopis2021-nb`
   - [link](https://www.nature.com/articles/s41592-021-01156-w)
-  - Guidelines and resources for accurate reporting of the most common fluorescence light microscopy techniques, emphasizing the impact of accurate microscopy metadata on data interpretation.'
+  - Guidelines and resources for accurate reporting of the most common fluorescence light microscopy techniques, emphasizing the impact of accurate microscopy metadata on data interpretation.
+* - 📄 Believing is seeing - the deceptive influence of bias in quantitative microscopy{cite}`Lee2024-zu`
+  - [link](https://doi.org/10.1242/jcs.261567)
+  - Thoughtful review on technological and especially psychological factors that can lead to biased microscopy results
 * - 🎥 iBiology Microscopy Short Course
   - [link](https://www.youtube.com/watch?v=4c5ILWQmqRY&list=PLQFc-Dxlf4pSRaEk8Xi9BzS0r8-LYmwRQ)
   - An 8 hour video series consisting of 14 videos introducting major concepts in microscopy. A longer course with >70 videos is also available. 

03_Image_analysis/Introduction.md

@@ -23,4 +23,6 @@ flowchart LR
  style G fill:#D6E6FF,stroke:#3A86FF
 ```
 
-The specifics of your workflow depend on your biological question. Below we present a few common types of analysis for fluorescence microscopy experiments. For each, we’ll explain key ideas to understand before you begin, common pitfalls, and links to a few key resources to learn more. We encourage you to think about your analysis strategy even before beginning sample preparation. While not always possible, speaking with an image analysis expert in your local core facility or asking a question on the [image.sc](https://image.sc) forum _before you begin_ can save you a ton of time and headache when it comes to designing an image analysis strategy.
+The specifics of your workflow depend on your biological question. Below we present a few common types of analysis for fluorescence microscopy experiments. For each, we’ll explain key ideas to understand before you begin, common pitfalls, and links to a few key resources to learn more. We encourage you to think about your analysis strategy even before beginning sample preparation. While not always possible, speaking with an image analysis expert{cite}`Cimini2024-uh` in your local core facility or asking a question on the [image.sc](https://image.sc) forum _before you begin_ can save you a ton of time and headache when it comes to designing an image analysis strategy. Some general concepts are also covered in a recent short review{cite}`.
+
+Note that "automated" and "quantified" are not at all the same as "accurate" "unbiased" - see {cite}`Jost2019-nx` and {cite}`Lee2024-zu` for further treatment of these issues.

03_Image_analysis/Resources.md

@@ -10,6 +10,9 @@
 * - 🌐 Image.sc {cite}`Rueden2019-qp`
   - [link](https://forum.image.sc/)
   - Discussion forum for bioimage analysis software
+* - 🌐 GloBIAS Bioimage Analyst Database
+  - [link](https://www.globias.org/resources/bioimage-analyst-db)
+  - Find the friendly local bioimage analyst near you!
 * - 🌐 Peter Bankhead’s Intro to Bioimage Analysis
   - [link](https://bioimagebook.github.io/)
   - Guide for absolute beginners to image analysis, including embedded questions/answers, exercises with Python and ImageJ, and videos to check understanding
@@ -22,7 +25,7 @@
 * - 📄 Made to measure: an introduction to quantification in microscopy data 
   - [link](https://arxiv.org/abs/2302.01657#) {cite}`Culley2023-dj`
   - An article describing several common classes of measurements made in microscopy data, as well as technical factors that may affect the results
-* - 🌐 Metrics Reloaded
+* - 🌐 Metrics Reloaded {cite}`Maier-Hein2024-cp,Reinke2024-aj,reinke2023common`
   - [link](https://metrics-reloaded.dkfz.de/)
   - An interactive guide to choosing the right metric for your scientific question
 * - 📄 A Hitchhiker's guide through the bio-image analysis software universe {cite}`Haase2022-ad`
@@ -49,4 +52,7 @@
 * - 🌐 Bioimage Analysis Notebooks
   - [link](https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/)
   - A collection of Python Jupyter notebooks for BioImageAnalysis, GPU-accelerated image processing, bio-image data science and more
+* - 📄 Believing is seeing - the deceptive influence of bias in quantitative microscopy{cite}`Lee2024-zu`
+  - [link](https://doi.org/10.1242/jcs.261567)
+  - Thoughtful review on technological and especially psychological factors that can lead to biased microscopy results
 ```

03_Image_analysis/SpecificUseSoftware.md

@@ -67,7 +67,7 @@ For documentation examples and  tutorials.
 ## <img src="https://us1.discourse-cdn.com/flex015/uploads/imagej/original/3X/3/f/3fe4d974194caabdb61a5574e24402db8484ab9b.png" alt="logo" width="30px"> Piximi
 
 
-[Piximi](https://www.piximi.app/) is an application for annotation and classification that runs entirely from your browser and requires no installation and minimal setup. 
+[Piximi](https://www.piximi.app/) {cite}`Moser2024-vt` is an application for annotation and classification that runs entirely from your browser and requires no installation and minimal setup. 
 
 
 ```{dropdown} What type of image analysis problem is it best at?

04_Data_presentation/Presentation_images.md

@@ -109,7 +109,7 @@ Missing explanations of image details/methods may result in non-reproducible dat
 
 ## Where can I learn more?
 
-Check out _Creating clear and informative image-based figures for scientific publications_{cite}`Jambor2021-qe` and _Community-developed checklists for publishing images and image analysis_{cite}`Schmied2023-ad` for more tips and best practices for making image figures. 
+Check out _Creating clear and informative image-based figures for scientific publications_{cite}`Jambor2021-qe` and _Community-developed checklists for publishing images and image analysis_{cite}`Schmied2024-et` for more tips and best practices for making image figures. 
 
 A cheat sheet on how to do basic image preparation with open source software: 
 

04_Data_presentation/Resources.md

@@ -10,8 +10,8 @@
 * - 📄 Creating clear and informative image-based figures for scientific publications {cite}`Jambor2021-qe`
   - [link](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001161 )
   - Review article on how to create accessible, fair scientific figures, including guidelines for microscopy images
-* - 📄 Community-developed checklists for publishing images and image analysis {cite}`Schmied2023-ad`
-  - [link](https://arxiv.org/abs/2302.07005)
+* - 📄 Community-developed checklists for publishing images and image analysis {cite}`Schmied2024-et`
+  - [link](https://doi.org/10.1038/s41592-023-01987-9)
   - A paper recommending checklists and best practices for publishing image data. [It also has a JupyterBook](https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html)
 * - 📖 Modern Statistics for Modern Biology {cite}`Holmes2019-no`
   - [link](https://www.huber.embl.de/msmb/)

community_resources.md

@@ -23,6 +23,9 @@ Below are globally and locally available community resources
 * - Scientific Community Image Forum (Image . sc) 
   - [link](https://forum.image.sc/)
   - Discussion forum for bioimage analysis software {cite}`Rueden2019-qp`
+* - Microtutor
+  - [link](https://microtutor.globalbioimaging.org/)
+  - A fantastic interactive course on fluorescence microscopy, created by the team at [Harvard CITE](https://cite.hms.harvard.edu/)
 * - HMS Nikon Imaging Center "Favorite References"
   - [link](https://nic.med.harvard.edu/fav_references/)
   - A curated list of references related to many aspects of microscopy and image analysis