Best AI tools for< Cell Biologist >

Deepcell is a company that develops technology for single-cell analysis. Their REM-I platform combines label-free imaging, deep learning, and gentle sorting to leverage single cell morphology as a high-dimensional quantitative readout. This allows researchers to gain insights into cells' phenotype and function to address important research questions across biology.

Byterat is a cloud-based platform that provides battery data management, visualization, and analytics. It offers an end-to-end data pipeline that automatically synchronizes, processes, and visualizes materials, manufacturing, and test data from all labs. Byterat also provides 24/7 access to experiments from anywhere in the world and integrates seamlessly with current workflows. It is customizable to specific cell chemistries and allows users to build custom visualizations, dashboards, and analyses. Byterat's AI-powered battery research has been published in leading journals, and its team has pioneered a new class of models that extract tell-tale signals of battery health from electrical signals to forecast future performance.

Tablesmith is a free, privacy-first, and intuitive spreadsheet automation tool that allows users to build reusable data flows, effortlessly sort, filter, group, format, or split data across files/sheets based on cell values. It is designed to be easy to learn and use, with a focus on privacy and cross-platform compatibility. Tablesmith also offers an AI autofill feature that suggests and fills in information based on the user's prompt.

PINNACLE is a flexible geometric deep learning approach that trains on contextualized protein interaction networks to generate context-aware protein representations. It provides protein representations split across various cell-type contexts from different tissues and organs. The tool can be fine-tuned to study the genomic effects of drugs and nominate promising protein targets and cell-type contexts for further investigation. PINNACLE exemplifies the paradigm of incorporating context-specific effects for studying biological systems, especially the impact of disease and therapeutics.

The 'machine-learning-research' repository is a comprehensive collection of resources related to mathematics, machine learning, deep learning, artificial intelligence, data science, and various scientific fields. It includes materials such as courses, tutorials, books, podcasts, communities, online courses, papers, and dissertations. The repository covers topics ranging from fundamental math skills to advanced machine learning concepts, with a focus on applications in healthcare, genetics, computational biology, precision health, and AI in science. It serves as a valuable resource for individuals interested in learning and researching in the fields of machine learning and related disciplines.

AITom is an open-source platform for AI-driven cellular electron cryo-tomography analysis. It is developed to process large amounts of Cryo-ET data, reconstruct, detect, classify, recover, and spatially model different cellular components using state-of-the-art machine learning approaches. The platform aims to automate cellular structure discovery and provide new insights into molecular biology and medical applications.

NoLabs is an open-source biolab that provides easy access to state-of-the-art models for bio research. It supports various tasks, including drug discovery, protein analysis, and small molecule design. NoLabs aims to accelerate bio research by making inference models accessible to everyone.

ceLLama is a streamlined automation pipeline for cell type annotations using large-language models (LLMs). It operates locally to ensure privacy, provides comprehensive analysis by considering negative genes, offers efficient processing speed, and generates customized reports. Ideal for quick and preliminary cell type checks.

Scientific Large Language Models (Sci-LLMs) is a repository that collects papers on scientific large language models, focusing on biology and chemistry domains. It includes textual, molecular, protein, and genomic languages, as well as multimodal language. The repository covers various large language models for tasks such as molecule property prediction, interaction prediction, protein sequence representation, protein sequence generation/design, DNA-protein interaction prediction, and RNA prediction. It also provides datasets and benchmarks for evaluating these models. The repository aims to facilitate research and development in the field of scientific language modeling.

LlamaBot is a Pythonic bot interface to Large Language Models (LLMs), providing an easy way to experiment with LLMs in Jupyter notebooks and build Python apps utilizing LLMs. It supports all models available in LiteLLM. Users can access LLMs either through local models with Ollama or by using API providers like OpenAI and Mistral. LlamaBot offers different bot interfaces like SimpleBot, ChatBot, QueryBot, and ImageBot for various tasks such as rephrasing text, maintaining chat history, querying documents, and generating images. The tool also includes CLI demos showcasing its capabilities and supports contributions for new features and bug reports from the community.

Awesome-Segment-Anything is a powerful tool for segmenting and extracting information from various types of data. It provides a user-friendly interface to easily define segmentation rules and apply them to text, images, and other data formats. The tool supports both supervised and unsupervised segmentation methods, allowing users to customize the segmentation process based on their specific needs. With its versatile functionality and intuitive design, Awesome-Segment-Anything is ideal for data analysts, researchers, content creators, and anyone looking to efficiently extract valuable insights from complex datasets.

cellseg-models.pytorch is a Python library built upon PyTorch for 2D cell/nuclei instance segmentation models. It provides multi-task encoder-decoder architectures and post-processing methods for segmenting cell/nuclei instances. The library offers high-level API to define segmentation models, open-source datasets for training, flexibility to modify model components, sliding window inference, multi-GPU inference, benchmarking utilities, regularization techniques, and example notebooks for training and finetuning models with different backbones.

**deep** doctection is a Python library that orchestrates document extraction and document layout analysis tasks using deep learning models. It does not implement models but enables you to build pipelines using highly acknowledged libraries for object detection, OCR and selected NLP tasks and provides an integrated framework for fine-tuning, evaluating and running models. For more specific text processing tasks use one of the many other great NLP libraries. **deep** doctection focuses on applications and is made for those who want to solve real world problems related to document extraction from PDFs or scans in various image formats. **deep** doctection provides model wrappers of supported libraries for various tasks to be integrated into pipelines. Its core function does not depend on any specific deep learning library. Selected models for the following tasks are currently supported: * Document layout analysis including table recognition in Tensorflow with **Tensorpack**, or PyTorch with **Detectron2**, * OCR with support of **Tesseract**, **DocTr** (Tensorflow and PyTorch implementations available) and a wrapper to an API for a commercial solution, * Text mining for native PDFs with **pdfplumber**, * Language detection with **fastText**, * Deskewing and rotating images with **jdeskew**. * Document and token classification with all LayoutLM models provided by the **Transformer library**. (Yes, you can use any LayoutLM-model with any of the provided OCR-or pdfplumber tools straight away!). * Table detection and table structure recognition with **table-transformer**. * There is a small dataset for token classification available and a lot of new tutorials to show, how to train and evaluate this dataset using LayoutLMv1, LayoutLMv2, LayoutXLM and LayoutLMv3. * Comprehensive configuration of **analyzer** like choosing different models, output parsing, OCR selection. Check this notebook or the docs for more infos. * Document layout analysis and table recognition now runs with **Torchscript** (CPU) as well and **Detectron2** is not required anymore for basic inference. * [**new**] More angle predictors for determining the rotation of a document based on **Tesseract** and **DocTr** (not contained in the built-in Analyzer). * [**new**] Token classification with **LiLT** via **transformers**. We have added a model wrapper for token classification with LiLT and added a some LiLT models to the model catalog that seem to look promising, especially if you want to train a model on non-english data. The training script for LayoutLM can be used for LiLT as well and we will be providing a notebook on how to train a model on a custom dataset soon. **deep** doctection provides on top of that methods for pre-processing inputs to models like cropping or resizing and to post-process results, like validating duplicate outputs, relating words to detected layout segments or ordering words into contiguous text. You will get an output in JSON format that you can customize even further by yourself. Have a look at the **introduction notebook** in the notebook repo for an easy start. Check the **release notes** for recent updates. **deep** doctection or its support libraries provide pre-trained models that are in most of the cases available at the **Hugging Face Model Hub** or that will be automatically downloaded once requested. For instance, you can find pre-trained object detection models from the Tensorpack or Detectron2 framework for coarse layout analysis, table cell detection and table recognition. Training is a substantial part to get pipelines ready on some specific domain, let it be document layout analysis, document classification or NER. **deep** doctection provides training scripts for models that are based on trainers developed from the library that hosts the model code. Moreover, **deep** doctection hosts code to some well established datasets like **Publaynet** that makes it easy to experiment. It also contains mappings from widely used data formats like COCO and it has a dataset framework (akin to **datasets** so that setting up training on a custom dataset becomes very easy. **This notebook** shows you how to do this. **deep** doctection comes equipped with a framework that allows you to evaluate predictions of a single or multiple models in a pipeline against some ground truth. Check again **here** how it is done. Having set up a pipeline it takes you a few lines of code to instantiate the pipeline and after a for loop all pages will be processed through the pipeline.

Yank Note is a highly extensible Markdown editor designed for productivity. It offers features like easy-to-use interface, powerful support for version control and various embedded content, high compatibility with local Markdown files, plug-in extension support, and encryption for saving private files. Users can write their own plug-ins to expand the editor's functionality. However, for more extendability, security protection is sacrificed. The tool supports sync scrolling, outline navigation, version control, encryption, auto-save, editing assistance, image pasting, attachment embedding, code running, to-do list management, quick file opening, integrated terminal, Katex expression, GitHub-style Markdown, multiple data locations, external link conversion, HTML resolving, multiple formats export, TOC generation, table cell editing, title link copying, embedded applets, various graphics embedding, mind map display, custom container support, macro replacement, image hosting service, OpenAI auto completion, and custom plug-ins development.

CoML (formerly MLCopilot) is an interactive coding assistant for data scientists and machine learning developers, empowered on large language models. It offers an out-of-the-box interactive natural language programming interface for data mining and machine learning tasks, integration with Jupyter lab and Jupyter notebook, and a built-in large knowledge base of machine learning to enhance the ability to solve complex tasks. The tool is designed to assist users in coding tasks related to data analysis and machine learning using natural language commands within Jupyter environments.

Foyle is a project focused on building agents to assist software developers in deploying and operating software. It aims to improve agent performance by collecting human feedback on agent suggestions and human examples of reasoning traces. Foyle utilizes a literate environment using vscode notebooks to interact with infrastructure, capturing prompts, AI-provided answers, and user corrections. The goal is to continuously retrain AI to enhance performance. Additionally, Foyle emphasizes the importance of reasoning traces for training agents to work with internal systems, providing a self-documenting process for operations and troubleshooting.

Chatbook is a paclet that adds support for LLM-powered notebooks to Wolfram. It allows users to interact with ChatGPT and generate immediately evaluatable Wolfram code. The code can be evaluated in place immediately, making it easy to explore and experiment with ideas.

The Neo4j GenAI Workshop repository contains notebooks for a workshop focusing on building a Neo4j Graph, text embedding, and providing demos for content generation. The workshop includes data staging, loading, and exploration using Cypher queries. It also covers improvements in LLM response quality, GPT-4 usage, and vector search speed. The repository has undergone multiple updates to enhance course quality, simplify content, and provide better explainers and examples.

EDA-AI is a repository containing implementations of cutting-edge research papers in the field of chip design. It includes DeepPlace, PRNet, HubRouter, and PreRoutGNN models for tasks such as placement, routing, timing prediction, and global routing. Researchers and practitioners can leverage these implementations to explore advanced techniques in chip design.

Jupyter AI connects generative AI with Jupyter notebooks. It provides a user-friendly and powerful way to explore generative AI models in notebooks and improve your productivity in JupyterLab and the Jupyter Notebook. Specifically, Jupyter AI offers: * An `%%ai` magic that turns the Jupyter notebook into a reproducible generative AI playground. This works anywhere the IPython kernel runs (JupyterLab, Jupyter Notebook, Google Colab, Kaggle, VSCode, etc.). * A native chat UI in JupyterLab that enables you to work with generative AI as a conversational assistant. * Support for a wide range of generative model providers, including AI21, Anthropic, AWS, Cohere, Gemini, Hugging Face, NVIDIA, and OpenAI. * Local model support through GPT4All, enabling use of generative AI models on consumer grade machines with ease and privacy.

This Code Interpreter SDK allows you to run AI-generated Python code and each run share the context. That means that subsequent runs can reference to variables, definitions, etc from past code execution runs. The code interpreter runs inside the E2B Sandbox - an open-source secure micro VM made for running untrusted AI-generated code and AI agents. - ✅ Works with any LLM and AI framework - ✅ Supports streaming content like charts and stdout, stderr - ✅ Python & JS SDK - ✅ Runs on serverless and edge functions - ✅ 100% open source (including infrastructure)

This repository contains community-driven practical examples of building AI applications and solving various tasks with AI using open-source tools and models. Everyone is welcome to contribute, and we value everybody's contribution! There are several ways you can contribute to the Open-Source AI Cookbook: Submit an idea for a desired example/guide via GitHub Issues. Contribute a new notebook with a practical example. Improve existing examples by fixing issues/typos. Before contributing, check currently open issues and pull requests to avoid working on something that someone else is already working on.

I assist biological image analysis, including ImageJ macro and Python coding.

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Expert in biology, always ready to clarify new stem cell treatments.biomedical research, clinical trials. Learn about different stem cell types, current/future uses, and the latest in research.

Expert on hydrogen production systems and the hydrogen economy.

A virtual smartphone repair manual offering detailed fixing instructions.

Allround electronics repair expert with practical advise and video resources on range of devices. Think circular, avoid e-waste.

Expert in all aspects of spectral flow cytometry.

Expert in SCLC research, focused on a specific paper and broader SCLC knowledge.

Everything about water-fuelled car