Miscellaneous
17,439 items in 132 lists
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We don't talk about Quarto apreshill.com
A blog post introducing Quarto publishing software by Alison Presmanes Hill.
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How to automatically convert TikZ images to SVG with Quarto andrewheiss.com
A blog post using the Pandoc diagram extension so TikZ diagrams render as SVG for HTML and Word, and as PDF for LaTeX output, by Andrew Heiss.
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How to Finally Fix Your Tables in Typst PDFs albert-rapp.de
A blog post on carrying custom gt table styling into Typst-rendered Quarto PDFs using a Lua filter by Albert Rapp.
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Tutorial: The ultimate guide to starting a Quarto blog albert-rapp.de
An in-depth guide on how to start blogging with Quarto.
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LeafByte zoegp.science
Free and open source mobile app for measuring herbivory quickly and accurately.
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Skimpy documentation aeturrell.github.io
Documentation made using quartodoc.
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YeastMate yeastmate.readthedocs.io
Neural network-assisted segmentation of mating and budding events in S. cerevisiae.
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VisionSetil visionsetil.com
Multi-view image classification of Iberian mushrooms for education (open encyclopedia of 523 taxa, deadly lookalikes). Orientation only — never consumption permission.
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TissUUmaps tissuumaps.github.io
Visualizer of NGS data, plot millions of points and interact, gate, export. ISS rounds and base visualization.
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Trackpy soft-matter.github.io
Fast and Flexible Particle-Tracking Toolkit.
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QuPath qupath.github.io
Open source software for digital pathology image analysis.
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RhizoTrak prbio-hub.github.io
Open source tool for flexible and efficient manual annotation of complex time-series minirhizotron images.
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Orbit orbit.bio
A versatile image analysis software for biological image-based quantification using machine learning, especially for whole slide imaging.
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Tutorial: Personal Website using Jupyter Notebook and Quarto adtarie.net
A Python-oriented step-by-step tutorial on how to create a website using Quarto.
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Large-scale image-based screening and profiling of cellular phenotypes onlinelibrary.wiley.com
A workflow for phenotype extraction from high throughput imaging experiments.
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Panda nitrc.org
Pipeline for Analyzing braiN Diffusion imAges: A MATLAB toolbox for pipeline processing of diffusion MRI images.
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MorphoGraphX morphographx.org
Open source application for the visualization and analysis of 4D biological datasets.
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PaCeQuant mitobo.informatik.uni-halle.de
An ImageJ-based tool which provides a fully automatic image analysis workflow for PC shape quantification.
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Biobeam maweigert.github.io
Open source software package that is designed to provide fast methods for in-silico optical experiments with an emphasize on image formation in biological tissues.
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Workflow and metrics for image quality control in large-scale high-content screens linkinghub.elsevier.com
Approaches for quality control in high-content imaging screens.
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NeuronJ imagescience.org
An ImageJ plugin for neurite tracing and analysis.
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TraJClassifier imagej.net
Fiji plugin that loads trajectories from TrackMate, characterizes them using TraJ and classifiies them into normal diffusion, subdiffusion, confined diffusion and directed/active motion by a random forest approach (through Renjin).
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PAT-GEOM ianzwchan.com
A software package for the analysis of animal colour pattern.
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HistoPLUS huggingface.co
Pre-trained model for cell nuclei segmentation and classification in histology images.
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TracX gitlab.com
MATLAB generic toolbox for cell tracking from various microscopy image modalities such as Bright-field (BF), phase contrast (PhC) or fluorescence (FL) with an automated track quality assessment in absence of a ground truth.
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Icy github.com
Open community platform for bioimage informatics, providing software resources to visualize, annotate and quantify bioimaging data.
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BABY git.ecdf.ed.ac.uk
An image processing pipeline for accurate single-cell growth estimation of budding cells from bright-field stacks.
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A Hitchhiker's guide through the bio-image analysis software universe febs.onlinelibrary.wiley.com
An article presenting a curated guide and glossary of bio-image analysis terms and tools.
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Biological imaging software tools dx.doi.org
The steps of biological image analysis and the appropriate tools for each step.
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BiofilmQ drescherlab.org
Advanced biofilm analysis tool for quantifying the properties of cells inside large 3-dimensional biofilm communities in space and time.
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BacStalk drescherlab.org
Interactive and user-friendly image analysis software tool to investigate the cell biology of common used bacterial species.
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Data-analysis strategies for image-based cell profiling doi.org
In-detail explanations of image analysis pipelines.
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CLIJ2 clij.github.io
GPU-accelerated image processing library for ImageJ/Fiji, Icy, MATLAB and Java.
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PyScratch bitbucket.org
Open source tool that autonomously performs quantitative analysis of in vitro scratch assays.
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BiaPy biapyx.github.io
Open source ready-to-use all-in-one library that provides deep-learning workflows for a large variety of bioimage analysis tasks.
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Vaa3D alleninstitute.org
Open-source software for 3D/4D/5D image visualization and analysis.
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WriteMage writemage.com
Native macOS app to use ChatGPT in any app. ($)
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DocGPT workspace.google.com
Writing assistant for Google Docs.
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wonderGPT wondergpt.co
Native macOS app with a focus on simplicity.
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Wielded wielded.com
Web UI that works for OpenAI, Azure, Anthropic, and AWS Bedrock. Free for individuals.
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Machato untimelyunicorn.gumroad.com
Native macOS app. ($)
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Stream data from ChatGPT with JavaScript umaar.com
Learn how to consume streaming data from ChatGPT using vanilla JavaScript.
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TypingMind typingmind.com
Alternative web UI.
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QuickGPT sindresorhus.gumroad.com
Access the ChatGPT web UI from the menu bar, Dock, or using a keyboard shortcut on macOS.
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Ask AI sindresorhus.com
Native watchOS app. ($)
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ScreenSnapAI screensnap.ai
Native macOS app to chat about captured screenshots. ($)
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Reddit reddit.com
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16x Prompt prompt.16x.engineer
Cross-platform app to add source code and formatting instructions into prompt for coding tasks. ($)
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Price Per Token pricepertoken.com
Compare LLM API pricing across providers. Includes token counter and cost calculator.
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Plus AI for Google Slides plusdocs.com
Create AI-powered presentations in Google Slides.
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