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Stefan Rödiger
@pangolin  ·  activity timestamp 3 hours ago

📢 @devTLB@mastodon.social and I’ve just published a review article titled **“Exploring Image Analysis in R: Applications and Advancements”** in *The R Journal* (Vol. 17, Issue 3).

🔍 The paper surveys #rstats image‑analysis packages, from the early work of *adimpro* and *EBImage* to the newer packages like *biopixR*. It shows that the majority of these packages are still active, with two‑thirds updated within the last 1.5 years. A robust and vibrant ecosystem for bioimage informatics.


📊 Key takeaways:


- Comprehensive overview of tools for multiplex imaging, cell tracking, and general-purpose analysis.

- Emphasis on end‑to‑end pipelines that extract meaningful biological insights from images.

- Real‑world examples demonstrating how R can address current scientific challenges in image analysis.


🔗 You can read the full article here: doi.org/10.32614/RJ-2025-030

I’m grateful for the support of my co‑authors Tim Brauckhoff, Julius Rublack. Feel free to share your thoughts or ask questions about applying these methods in your own work!

Image from 'Exploring Image Analysis in R' by Brauckhoff et al. The image contains two parts: Figure 12 and Figure 13.  Figure 12 displays two fluorescence microscopy images of cells with stained nuclei. In image A, the nuclei are blue, and DNA double-strand breaks (H2AX foci) are highlighted in red. Image B shows a similar view but with different color highlighting. Figure 13 is a bar graph showing the frequency distribution of gamma H2AX foci counts per cell. The x-axis represents foci count (0 to 20), and the y-axis represents frequency.
Image from 'Exploring Image Analysis in R' by Brauckhoff et al. The image contains two parts: Figure 12 and Figure 13. Figure 12 displays two fluorescence microscopy images of cells with stained nuclei. In image A, the nuclei are blue, and DNA double-strand breaks (H2AX foci) are highlighted in red. Image B shows a similar view but with different color highlighting. Figure 13 is a bar graph showing the frequency distribution of gamma H2AX foci counts per cell. The x-axis represents foci count (0 to 20), and the y-axis represents frequency.
Image from 'Exploring Image Analysis in R' by Brauckhoff et al. The image contains two parts: Figure 12 and Figure 13. Figure 12 displays two fluorescence microscopy images of cells with stained nuclei. In image A, the nuclei are blue, and DNA double-strand breaks (H2AX foci) are highlighted in red. Image B shows a similar view but with different color highlighting. Figure 13 is a bar graph showing the frequency distribution of gamma H2AX foci counts per cell. The x-axis represents foci count (0 to 20), and the y-axis represents frequency.
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