Blog post (28)

Blog post (28)#

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

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

Content type: Blog Post

https://cs231n.github.io/convolutional-networks/

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 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

Content type: Blog Post

https://observablehq.com/blog/effective-animation

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 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

Content type: Blog Post

https://www.nature.com/articles/d41586-023-03064-9

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/

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

Content type: Blog Post

https://www.tdda.info/name-styles

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

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

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

Content type: Blog Post

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

Blog post (28)

Contents

Blog post (28)#

Annotating 3D images in napari#

Biologists, stop putting UMAP plots in your papers#

Browsing the Open Microscopy Image Data Resource with Python#

CS231n Convolutional Neural Networks for Visual Recognition#

Collaborative bio-image analysis script editing with git#

Creating a Research Data Management Plan using chatGPT#

DL4MicEverywhere – Overcoming reproducibility challenges in deep learning microscopy imaging#

Data Visualization with Flying Colors#

Data handling in large-scale electron microscopy#

Feature extraction in napari#

Five great reasons to share your research data#

Five ways to effectively use animation in data visualization#

Getting started with Mambaforge and Python#

How open-source software could finally get the world’s microscopes speaking the same language#

How to write a bug report#

If you license it, it’ll be harder to steal it. Why we should license our work#

Managing Scientific Python environments using Conda, Mamba and friends#

Name Styles#

New report highlights the scientific impact of open source software#

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

Prompt Engineering in Bio-image Analysis#

Quality assurance of segmentation results#

Rescaling images and pixel (an)isotropy#

Running Deep-Learning Scripts in the BiA-PoL Omero Server#

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

Sharing research data with Zenodo#

Things that shouldn’t be in file names for $1000 Alex#

Tracking in napari#