Blog post (23)

Blog post (23)#

Annotating 3D images in napari#

Mara Lampert

Tags: Python, Napari, Bioimage Analysis

Content type: Blog Post

https://focalplane.biologists.com/2023/03/30/annotating-3d-images-in-napari/

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

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

Content type: Blog Post

https://biapol.github.io/blog/robert_haase/browsing_idr/readme.html

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

Content type: Blog Post

https://focalplane.biologists.com/2021/09/04/collaborative-bio-image-analysis-script-editing-with-git/

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

Content type: Blog Post

https://focalplane.biologists.com/2023/11/06/creating-a-research-data-management-plan-using-chatgpt/

DL4MicEverywhere – Overcoming reproducibility challenges in deep learning microscopy imaging#

Iván Hidalgo-Cenalmor

Published 2024-07-29

Licensed UNKNOWN

Tags: Bio Image Analysis, Artifical Intelligence

Content type: Blog Post

https://focalplane.biologists.com/2024/07/29/dl4miceverywhere-overcoming-reproducibility-challenges-in-deep-learning-microscopy-imaging/

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

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

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

Content type: Blog Post

https://focalplane.biologists.com/2023/05/03/feature-extraction-in-napari/

Five great reasons to share your research data#

Published 2022-03-18

Licensed UNKNOWN

Sharing your data can benefit your career in some interesting ways. In this post, read why you should be making more of your research data openly available.

Tags: Research Data Management, Sharing

Content type: Blog Post

https://web.library.uq.edu.au/blog/2022/03/five-great-reasons-share-your-research-data

Getting started with Mambaforge and Python#

Mara Lampert

Licensed CC-BY-4.0

Tags: Python, Conda, Mamba

Content type: Blog Post

https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html

How to write a bug report#

Mara Lampert

Tags: Github, Python, Science Communication

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

Content type: Blog Post

https://focalplane.biologists.com/2023/05/06/if-you-license-it-itll-be-harder-to-steal-it-why-we-should-license-our-work/

Managing Scientific Python environments using Conda, Mamba and friends#

Robert Haase

Licensed CC-BY-4.0

Tags: Python, Conda, Mamba

Content type: Blog Post

https://focalplane.biologists.com/2022/12/08/managing-scientific-python-environments-using-conda-mamba-and-friends/

New report highlights the scientific impact of open source software#

UNKNOWN

Published UNKNOWN

Licensed UNKNOWN

Tags: Open Source, Alphafold

Content type: Report, Blog Post

https://www.statnews.com/sponsor/2024/11/26/new-report-highlights-the-scientific-impact-of-open-source-software/

Promoting Data Management at the Nikon Imaging Center and Cell Biology Microscopy Facility#

Jennifer Waters

Tags: Research Data Management

Content type: Blog Post

https://datamanagement.hms.harvard.edu/news/promoting-data-management-nikon-imaging-center-and-cell-biology-microscopy-facility

Prompt Engineering in Bio-image Analysis#

Mara Lampert

Tags: Python, Jupyter, Bioimage Analysis, Prompt Engineering, Biabob

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

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

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

Content type: Blog Post

https://biapol.github.io/blog/marcelo_zoccoler/omero_scripts/readme.html

Sharing Your Poster on Figshare: A Community Guide to How-To and Why#

Elisabeth Kugler

Tags: Sharing, Research Data Management

Content type: Blog Post

https://focalplane.biologists.com/2023/07/26/sharing-your-poster-on-figshare/

Sharing research data with Zenodo#

Robert Haase

Licensed CC-BY-4.0

Blog post about how to share data using zenodo.org

Tags: Sharing, Research Data Management

Content type: Blog Post

https://focalplane.biologists.com/2023/02/15/sharing-research-data-with-zenodo/

Tracking in napari#

Mara Lampert

Tags: Python, Napari, Bioimage Analysis

Content type: Blog Post

https://focalplane.biologists.com/2023/06/01/tracking-in-napari/