Blog post (34)#
Annotating 3D images in napari#
Mara Lampert
Tags: Python, Napari, Bioimage Analysis, Include In Dalia
Content type: Blog Post
https://focalplane.biologists.com/2023/03/30/annotating-3d-images-in-napari/
Autopilot, Copilot, and Software Developers#
Rahul Pandita
Published 2025-10-12
Licensed UNKNOWN
Language models (LLMs) are rapidly becoming essential developer tools. But the metaphors we use to describe them matter. One often used is: “LLMs are the autopilot of coding.” As both a developer and a pilot, that metaphor misses the mark on several levels. This blog post pens down why “Copilot” is a far better analogy than “autopilot” when it comes to LLMs and vibe coding.
Tags: Artificial Intelligence, Include In Dalia
Content type: Blog Post
Biologists, stop putting UMAP plots in your papers#
Rafael Irizarry
Published 2024-12-23
Licensed UNKNOWN
UMAP is a powerful tool for exploratory data analysis, but without a clear understanding of how it works, it can easily lead to confusion and misinterpretation.
Tags: Biology, Data Analysis, Umap, Exclude From Dalia
Content type: Blog Post
https://simplystatistics.org/posts/2024-12-23-biologists-stop-including-umap-plots-in-your-papers/
Browsing the Open Microscopy Image Data Resource with Python#
Robert Haase
Licensed CC-BY-4.0
Tags: OMERO, Python, Include In Dalia
Content type: Blog Post
https://biapol.github.io/blog/robert_haase/browsing_idr/readme.html
CS231n Convolutional Neural Networks for Visual Recognition#
Geeth Sethi, Sumith Kulal, Kevin Zakka, William Shen, Rachel Gardner
Licensed UNKNOWN
ConvNet architectures make the explicit assumption that the inputs are images, which allows us to encode certain properties into the architecture. These then make the forward function more efficient to implement and vastly reduce the amount of parameters in the network.
Tags: Deep Learning, Computer Vision, Neural Networks, Machine Learning, Include In Dalia
Content type: Blog Post
Collaborative bio-image analysis script editing with git#
Robert Haase
Licensed CC-BY-4.0
Introduction to version control using git for collaborative, reproducible script editing.
Tags: Sharing, Research Data Management, Include In Dalia
Content type: Blog Post
Creating a Research Data Management Plan using chatGPT#
Robert Haase
Published 2023-11-06
Licensed CC-BY-4.0
In this blog post the author demonstrates how chatGPT can be used to combine a fictive project description with a DMP specification to produce a project-specific DMP.
Tags: Research Data Management, Artificial Intelligence, Include In Dalia
Content type: Blog Post
https://focalplane.biologists.com/2023/11/06/creating-a-research-data-management-plan-using-chatgpt/
DAFT: minimal principles for reproducible research papers#
Bruno C. Vellutini
Published 2026-01-05
Licensed CC-BY-SA-4.0
A minimal set of principles for organizing research papers.
Tags: Reproducibility, Fair Principles, Research Data Management, Include In Dalia
Content type: Blog Post
DL4MicEverywhere – Overcoming reproducibility challenges in deep learning microscopy imaging#
Iván Hidalgo-Cenalmor
Published 2024-07-29
Licensed UNKNOWN
Tags: Bio Image Analysis, Artifical Intelligence, Include In Dalia
Content type: Blog Post
Data Visualization with Flying Colors#
Joachim Goedhart
Published 2019-08-29
Licensed UNKNOWN
The author discusses a number of color palettes that are suitable for coloring graphical elements in plots.
Tags: Data Visualization, Include In Dalia
Content type: Blog Post
https://thenode.biologists.com/data-visualization-with-flying-colors/research/
Data handling in large-scale electron microscopy#
Job Fermie
Tags: Research Data Management, Include In Dalia
Content type: Blog Post
https://blog.delmic.com/data-handling-in-large-scale-electron-microscopy
Feature extraction in napari#
Mara Lampert
Tags: Python, Napari, Bioimage Analysis, Include In Dalia
Content type: Blog Post
https://focalplane.biologists.com/2023/05/03/feature-extraction-in-napari/
Five ways to effectively use animation in data visualization#
Robert Kosara, Allison Horst
Published 2024-12-05
Licensed UNKNOWN
This post explores how animation can enhance data visualizations by improving viewer understanding and engagement, while also acknowledging the risks of misuse. It presents five practical techniques, supported by examples and implementation tips using D3 or Observable Plot.
Tags: Data Visualization, Include In Dalia
Content type: Blog Post
From Click to Code: Reproducibility in Bio-image Analysis#
Mara Lampert
Published 2025-08-05
Licensed CC-BY-4.0
This blog post revolves around reproducibility in bio-image analysis across several popular platforms, including Napari, Fiji, QuPath, Galaxy, CellProfiler and JIPipe.
Tags: Bioimage Analysis, Include In Dalia
Content type: Blog Post
Getting started with Mambaforge and Python#
Mara Lampert
Licensed CC-BY-4.0
Tags: Python, Conda, Mamba, Include In Dalia
Content type: Blog Post
https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html
How open-source software could finally get the world’s microscopes speaking the same language#
Michael Brooks
Published 2023-10-02
Licensed UNKNOWN
A plethora of standards mean shareable and verifiable microscopy data often get lost in translation. Biologists are working on a solution.
Tags: Research Data Management, Microscopy, Exclude From Dalia
Content type: Blog Post
How to write a bug report#
Mara Lampert
Tags: Github, Python, Science Communication, Include In Dalia
Content type: Blog Post
https://focalplane.biologists.com/2024/04/03/how-to-write-a-bug-report/
If you license it, it’ll be harder to steal it. Why we should license our work#
Robert Haase
Licensed CC-BY-4.0
Blog post about why we should license our work and what is important when choosing a license.
Tags: Licensing, Research Data Management, Include In Dalia
Content type: Blog Post
Managing Scientific Python environments using Conda, Mamba and friends#
Robert Haase
Licensed CC-BY-4.0
Tags: Python, Conda, Mamba, Include In Dalia
Content type: Blog Post
Name Styles#
Nick Radcliffe
Published None
Licensed UNKNOWN
This playful exploration delves into the quirky world of naming conventions in computing and data, humorously comparing them to Boston Box matrices and D&D alignments while poking fun at the chaos of categorizing what makes sense in metadata standards.
Tags: Research Data Management, Include In Dalia
Content type: Blog Post
New report highlights the scientific impact of open source software#
UNKNOWN
Published UNKNOWN
Licensed UNKNOWN
Tags: Open Source, Alphafold, Exclude From Dalia
Content type: Report, Blog Post
OMERO Outputs: Insights from the 4th BioHackathon 2025#
Lea Kabjesz
Licensed CC-BY-4.0
Tags: Microscopy Analysis, Hackathon, Bioimaging, OMERO
Content type: Blog Post
https://focalplane.biologists.com/2025/12/17/omero-outputs-insights-from-the-4th-biohackathon-2025/
Promoting Data Management at the Nikon Imaging Center and Cell Biology Microscopy Facility#
Jennifer Waters
Tags: Research Data Management, Include In Dalia
Content type: Blog Post
Prompt Engineering in Bio-image Analysis#
Mara Lampert
Tags: Python, Jupyter, Bioimage Analysis, Prompt Engineering, Biabob, Include In Dalia
Content type: Blog Post
https://focalplane.biologists.com/2024/07/18/prompt-engineering-in-bio-image-analysis/
Quality assurance of segmentation results#
Mara Lampert
Tags: Python, Napari, Bioimage Analysis, Include In Dalia
Content type: Blog Post
https://focalplane.biologists.com/2023/04/13/quality-assurance-of-segmentation-results/
Rescaling images and pixel (an)isotropy#
Mara Lampert
Tags: Python, Napari, Bioimage Analysis, Include In Dalia
Content type: Blog Post
https://focalplane.biologists.com/2023/03/02/rescaling-images-and-pixel-anisotropy/
Running Deep-Learning Scripts in the BiA-PoL Omero Server#
Marcelo Zoccoler
Licensed CC-BY-4.0
Tags: Python, Artificial Intelligence, Bioimage Analysis, Include In Dalia
Content type: Blog Post
https://biapol.github.io/blog/marcelo_zoccoler/omero_scripts/readme.html
The Illustrated Stable Diffusion#
Jay Alammar
Published 2022-10-04
Licensed CC-BY-NC-SA-4.0
AI image generation is the most recent AI capability blowing people’s minds (mine included). The ability to create striking visuals from text descriptions has a magical quality to it and points clearly to a shift in how humans create art. The release of Stable Diffusion is a clear milestone in this development because it made a high-performance model available to the masses.
Tags: Artificial Intelligence, Include In Dalia
Content type: Blog Post
Things that shouldn’t be in file names for $1000 Alex#
Joseph Scott
Published 2007-02-12
Licensed UNKNOWN
In this blog post, the author emphasizes problematic characters (e.g., spaces, slashes, colons) that should be avoided in filenames to ensure cross-platform compatibility across operating systems like Windows, macOS, and Linux, emphasizing the chaos caused by differing filesystem rules and naming conventions.
Tags: Reseach Data Management, Include In Dalia
Content type: Blog Post
https://blog.josephscott.org/2007/02/12/things-that-shouldnt-be-in-file-names-for-1000-alex/
Tracking in napari#
Mara Lampert
Tags: Python, Napari, Bioimage Analysis, Include In Dalia
Content type: Blog Post
https://focalplane.biologists.com/2023/06/01/tracking-in-napari/
When To Say “Good Enough”#
Beth Cimini
Published 2019-10-21
Licensed CC-BY-4.0
Blog post from the “Measure Everything… Ask Questions Later” blog of the Broad Institute Imaging Platform. How do I know when my analysis workflow is doing well enough at finding the objects or measuring the things I care about?
Tags: Bioimage Analysis, Include In Dalia
Content type: Blog Post
https://zenodo.org/records/10498985