# Notebook (57) ## 2022 MIC Workshop on Bioimage processing with Python Guillaume Witz Licensed UNKNOWN Tags: Python, Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/guiwitz/MICPy_Workshop_2022](https://github.com/guiwitz/MICPy_Workshop_2022) --- ## A Fiji Scripting Tutorial Albert Cardona Licensed CC0-1.0 Tags: Imagej, Bioimage Analysis, Include In Dalia Content type: Notebook [https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial/](https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial/) --- ## Bio-image Data Science Robert Haase Licensed CC-BY-4.0 This repository contains training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python. Tags: Research Data Management, Artificial Intelligence, Bioimage Analysis, Python, Include In Dalia Content type: Notebook [https://github.com/ScaDS/BIDS-lecture-2024](https://github.com/ScaDS/BIDS-lecture-2024) --- ## Bio-image analysis, biostatistics, programming and machine learning for computational biology Anna Poetsch, Biotec Dresden, Marcelo Leomil Zoccoler, Johannes Richard Müller, Robert Haase Licensed CC-BY-4.0 Tags: Python, Bioimage Analysis, Napari, Include In Dalia Content type: Notebook [https://github.com/BiAPoL/Bio-image_Analysis_with_Python](https://github.com/BiAPoL/Bio-image_Analysis_with_Python) --- ## BioImage Analysis Notebooks Robert Haase et al. Licensed ['CC-BY-4.0', 'BSD-3-CLAUSE'] Tags: Python, Bioimage Analysis, Include In Dalia Content type: Book, Notebook [https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/intro.html](https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/intro.html) --- ## CARE/Stardist tutorials for EMBO Practical Course — Computational optical biology 2022 Martin Weigert Licensed UNKNOWN Tags: Python, Artificial Intelligence, Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/maweigert/embo_2022](https://github.com/maweigert/embo_2022) --- ## CSBDeep and StarDist @ I2K 2020 Martin Weigert, Uwe Schmidt Licensed UNKNOWN Tags: Python, Artificial Intelligence, Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/maweigert/stardist-i2k](https://github.com/maweigert/stardist-i2k) --- ## CellProfiler tutorials Licensed BSD-3-CLAUSE CellProfiler tutorials and guided exercises about translocation, segmentation, pixel-based classification and quality control Tags: Cellprofiler, Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/CellProfiler/tutorials](https://github.com/CellProfiler/tutorials) --- ## CellTrackColab Guillaume Jacquemet Licensed MIT Tags: Exclude From Dalia Content type: Notebook, Collection [https://www.biorxiv.org/content/10.1101/2023.10.20.563252v2](https://www.biorxiv.org/content/10.1101/2023.10.20.563252v2) [https://github.com/guijacquemet/CellTracksColab](https://github.com/guijacquemet/CellTracksColab) --- ## Community-developed checklists for publishing images and image analyses Beth Cimini et al. Licensed BSD-3-CLAUSE This book is a companion to the Nature Methods publication Community-developed checklists for publishing images and image analyses. In this paper, members of QUAREP-LiMi have proposed 3 sets of standards for publishing image figures and image analysis - minimal requirements, recommended additions, and ideal comprehensive goals. By following this guidance, we hope to remove some of the stress non-experts may face in determining what they need to do, and we also believe that researchers will find their science more interpretable and more reproducible. Tags: Bioimage Analysis, Research Data Management, Include In Dalia Content type: Notebook, Collection [https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html](https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html) --- ## Course on Deep Learning for imaging using PyTorch Guillaume Witz Licensed UNKNOWN Tags: Python, Bioimage Analysis, Artificial Intelligence, Include In Dalia Content type: Notebook [https://github.com/guiwitz/DLImaging](https://github.com/guiwitz/DLImaging) --- ## DEEP NAPARI : Napari as a tool for deep learning project management Herearii Metuarea, David Rousseau, Pejman Rasti, Valentin Gilet Licensed UNKNOWN Tags: Artificial Intelligence, Bioimage Analysis, Exclude From Dalia Content type: Notebook [https://github.com/hereariim/DEEP-NAPARI](https://github.com/hereariim/DEEP-NAPARI) --- ## DL4MicEverywhere Iván Hidalgo, et al. Licensed CC-BY-4.0 Tags: Bioimage Analysis, Exclude From Dalia Content type: Notebook, Collection [https://github.com/HenriquesLab/DL4MicEverywhere](https://github.com/HenriquesLab/DL4MicEverywhere) --- ## DL@MBL 2021 Exercises Jan Funke, Constantin Pape, Morgan Schwartz, Xiaoyan Licensed UNKNOWN Tags: Artificial Intelligence, Bioimage Analysis, Exclude From Dalia Content type: Slides, Notebook [https://github.com/JLrumberger/DL-MBL-2021](https://github.com/JLrumberger/DL-MBL-2021) --- ## Dask Course Guillaume Witz Licensed UNKNOWN Tags: Python, Bioimage Analysis, Big Data, Exclude From Dalia Content type: Notebook [https://github.com/guiwitz/DaskCourse](https://github.com/guiwitz/DaskCourse) --- ## Deep Learning Based Segmentation For Biologists Licensed AGPL-3.0 Tags: Python, R, Artificial Intelligence, Include In Dalia Content type: Notebook [https://github.com/tpecot/DeepLearningBasedSegmentationForBiologists/](https://github.com/tpecot/DeepLearningBasedSegmentationForBiologists/) --- ## Deep Learning for image analysis - Exercises Martin Weigert Licensed UNKNOWN Tags: Fiji, Artificial Intelligence, Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/maweigert/zidas_2020_DL_intro_Part_2](https://github.com/maweigert/zidas_2020_DL_intro_Part_2) --- ## Deep Vision and Graphics Victor Yurchenko, Fedor Ratnikov, Viktoriia Checkalina Licensed MIT Tags: Python, Artificial Intelligence, Include In Dalia Content type: Notebook [https://github.com/yandexdataschool/deep_vision_and_graphics](https://github.com/yandexdataschool/deep_vision_and_graphics) --- ## EMBL Deep Learning course 2019 exercises and materials Valentyna Zinchenko, Pejman Rasti, Martin Weigert, Szymon Stoma Licensed UNKNOWN Tags: Python, Artificial Intelligence, Include In Dalia Content type: Notebook [https://github.com/kreshuklab/teaching-dl-course-2019](https://github.com/kreshuklab/teaching-dl-course-2019) --- ## EMBL Deep Learning course 2021/22 exercises and materials Martin Weigert, Constantin Pape Licensed UNKNOWN Tags: Python, Artificial Intelligence, Include In Dalia Content type: Notebook [https://github.com/kreshuklab/teaching-dl-course-2022](https://github.com/kreshuklab/teaching-dl-course-2022) --- ## EMBL Deep Learning course 2023 exercises and materials Martin Weigert, Uwe Schmidt, Benjamin Gallusser, Albert Dominguez Mantes, Buglakova Alyona Licensed UNKNOWN Tags: Python, Artificial Intelligence, Include In Dalia Content type: Notebook [https://github.com/kreshuklab/teaching-dl-course-2023](https://github.com/kreshuklab/teaching-dl-course-2023) --- ## Elastix tutorial Marvin Albert Licensed BSD-3-CLAUSE Tutorial material for teaching the basics of (itk-)elastix for image registration in microscopy images. Tags: Image Registration, Itk, Elastix, Include In Dalia Content type: Notebook, Collection [https://m-albert.github.io/elastix_tutorial/intro.html](https://m-albert.github.io/elastix_tutorial/intro.html) --- ## Fundamentals in digital image processing Guillaume Witz Licensed UNKNOWN Tags: Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/guiwitz/Fundamentals_image_processing](https://github.com/guiwitz/Fundamentals_image_processing) --- ## Fundamentals of image analysis in Python with scikit-image, napari, and friends Juan Nunez-Iglesias Licensed BSD-3-CLAUSE Tags: Python, Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/jni/halfway-to-i2k-skimage-napari](https://github.com/jni/halfway-to-i2k-skimage-napari) --- ## I2K 2024: clEsperanto - GPU-Accelerated Image Processing Library Stephane Rigaud, Robert Haase Licensed BSD-3-CLAUSE Course and material for the clEsperanto workshop presented at I2K 2024 @ Human Technopol (Milan, Italy). The workshop is an hands-on demo of the clesperanto project, focussing on how to use the library for users who want use GPU-acceleration for their Image Processing pipeline. Tags: Bioimage Analysis, Include In Dalia Content type: Github Repository, Workshop, Tutorial, Notebook [https://github.com/StRigaud/clesperanto_workshop_I2K24?tab=readme-ov-file](https://github.com/StRigaud/clesperanto_workshop_I2K24?tab=readme-ov-file) --- ## I2K2024 workshop material - Lazy Parallel Processing and Visualization of Large Data with ImgLib2, BigDataViewer, the N5-API, and Spark Stephan Saalfeld, Tobias Pietzsch Published None Licensed APACHE-2.0 Tags: Bioimage Analysis, Include In Dalia Content type: Workshop, Notebook, Github Repository [https://saalfeldlab.github.io/i2k2024-lazy-workshop/](https://saalfeldlab.github.io/i2k2024-lazy-workshop/) [https://github.com/saalfeldlab/i2k2024-lazy-workshop](https://github.com/saalfeldlab/i2k2024-lazy-workshop) --- ## I2K2024(virtual) - Bio-Image Analysis Code Generation Robert Haase Licensed BSD-3-CLAUSE This repository contains training materials for the Tutorial "Bio-Image Analysis Code Generation" at the From Images To Knowledge (I2K) Conference (virtual) October 28th-30th 2024. Tags: Bioimage Analysis, Notebooks, Biabob, Include In Dalia Content type: Github Repository, Tutorial, Notebook [https://github.com/haesleinhuepf/i2k2024-ai-code-generation](https://github.com/haesleinhuepf/i2k2024-ai-code-generation) --- ## IAFIG-RMS Python for Bioimage Analysis Course Aurelien Barbotin, Chas Nelson, Dominic Waithe, Ola (Alexandra) Tarkowska, Mikolaj Kundegorski, Stephen Cross, Todd Fallesen Licensed GPL-3.0 Tags: Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/RMS-DAIM/Python-for-Bioimage-Analysis](https://github.com/RMS-DAIM/Python-for-Bioimage-Analysis) --- ## Image analysis and visualization in Python with scikit-image, napari, and friends Juan Nunez-Iglesias Licensed BSD-3-CLAUSE Tags: Python, Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/scipy-2023-image-analysis/tutorial](https://github.com/scipy-2023-image-analysis/tutorial) --- ## Image processing for beginners Guillaume Witz Licensed BSD-3-CLAUSE Tags: Python, Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/guiwitz/PyImageCourse_beginner](https://github.com/guiwitz/PyImageCourse_beginner) --- ## Image processing with Python Guillaume Witz Licensed MIT Series of Notebooks exposing how to do mostly basic and some advanced image processing using Python. It uses standard packages (Numpy, Maplotlib) and for the image processing parts is heavily based on the scikit-image package. Tags: Python, Include In Dalia Content type: Notebook [https://github.com/guiwitz/Python_image_processing](https://github.com/guiwitz/Python_image_processing) --- ## Introduction to Bioimage Analysis Pete Bankhead Licensed CC-BY-4.0 Tags: Python, Imagej, Bioimage Analysis, Include In Dalia Content type: Book, Notebook [https://bioimagebook.github.io/index.html](https://bioimagebook.github.io/index.html) --- ## Introduction to Deep Learning for Microscopy Costantin Pape Licensed MIT This course consists of lectures and exercises that teach the background of deep learning for image analysis and show applications to classification and segmentation analysis problems. Tags: Artificial Intelligence, Python, Include In Dalia Content type: Notebook [https://github.com/computational-cell-analytics/dl-for-micro](https://github.com/computational-cell-analytics/dl-for-micro) --- ## Lecture-materials of the DeepLife course Carl Herrmann, annavonbachmann, David Hoksza, Martin Schätz, Dario Malchiodi, jnguyenvan, Britta Velten, Elodie Laine, JanaBraunger, barwil Published 2023-12-06 Licensed UNKNOWN Tags: Bioinformatics, Exclude From Dalia Content type: Github Repository, Slides, Notebook [https://github.com/deeplife4eu/Lecture-materials/](https://github.com/deeplife4eu/Lecture-materials/) --- ## Materials for EMBL Coding Club Mini-Tutorials Jonas Hartmann, et al. Licensed UNKNOWN Tags: Python, Exclude From Dalia Content type: Code, Notebook [https://github.com/WhoIsJack/EMBL-CodingClub](https://github.com/WhoIsJack/EMBL-CodingClub) [https://bio-it.embl.de/Coding%20Club/Curated%20Tutorials/](https://bio-it.embl.de/Coding%20Club/Curated%20Tutorials/) --- ## Metabolic networks modelling with COBRApy Karin Sasaki, Aleksej Zelezniak Licensed UNKNOWN Tags: Python, Include In Dalia Content type: Notebook [https://github.com/karinsasaki/metabolic-networks-modelling](https://github.com/karinsasaki/metabolic-networks-modelling) --- ## NEUBIAS Academy @HOME: Interactive Bioimage Analysis with Python and Jupyter Licensed BSD-3-CLAUSE Tags: Python, Neubias, Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/guiwitz/neubias_academy_biapy](https://github.com/guiwitz/neubias_academy_biapy) --- ## NEUBIAS Analyst School 2018 Assaf Zaritsky, Csaba Molnar, Vasja Urbancic, Richard Butler, Anna Kreshuk, Vannary Meas-Yedid Licensed UNKNOWN Tags: Neubias, Bioimage Analysis, Include In Dalia Content type: Slides, Code, Notebook [https://github.com/miura/NEUBIAS_AnalystSchool2018](https://github.com/miura/NEUBIAS_AnalystSchool2018) --- ## NEUBIAS Bioimage Analyst School 2019 Kota Miura, Chong Zhang, Jean-Yves Tinevez, Robert Haase, Julius Hossein, Pejamn Rasti, David Rousseau, Ignacio Arganda-Carreras, Siân Culley, et al. Licensed UNKNOWN Tags: Neubias, Bioimage Analysis, Include In Dalia Content type: Slides, Code, Notebook [https://github.com/miura/NEUBIAS_AnalystSchool2019](https://github.com/miura/NEUBIAS_AnalystSchool2019) --- ## NEUBIAS Bioimage Analyst School 2020 Marion Louveaux, Stéphane Verger, Arianne Bercowsky Rama, Ignacio Arganda-Carreras, Estibaliz Gómez-de-Mariscal, Kota Miura, et al. Licensed UNKNOWN Tags: Neubias, Bioimage Analysis, Include In Dalia Content type: Slides, Code, Notebook [https://github.com/miura/NEUBIAS_AnalystSchool2020](https://github.com/miura/NEUBIAS_AnalystSchool2020) --- ## Neubias Academy 2020: Introduction to Nuclei Segmentation with StarDist Martin Weigert, Olivier Burri, Siân Culley, Uwe Schmidt Licensed UNKNOWN Tags: Python, Neubias, Artificial Intelligence, Bioimage Analysis, Include In Dalia Content type: Slides, Notebook [https://github.com/maweigert/neubias_academy_stardist](https://github.com/maweigert/neubias_academy_stardist) --- ## ONBI Image Analysis Course Mark Jenkinson, Jens Rittscher, Dominic Waithe Licensed GPL-2.0 This repository contains the materials for the University of Oxford DTC ONBI Image Analysis course. Tags: Python, Bioimage Analysis, Include In Dalia Content type: Notebook [https://github.com/dwaithe/ONBI_image_analysis](https://github.com/dwaithe/ONBI_image_analysis) --- ## Open Image Data Handbook Kevin Yamauchi Licensed CC-BY-4.0 Tags: Neubias, Research Data Management, Napari, Python, Bioimage Analysis, Include In Dalia Content type: Book, Notebook [https://kevinyamauchi.github.io/open-image-data/intro.html](https://kevinyamauchi.github.io/open-image-data/intro.html) --- ## PoL Bio-Image Analysis Early Career Bio-image Analysis Training School Tags: Bioimage Analysis, Python, Include In Dalia Content type: Event, Notebook [https://biapol.github.io/PoL-BioImage-Analysis-TS-Early-Career-Track/intro.html](https://biapol.github.io/PoL-BioImage-Analysis-TS-Early-Career-Track/intro.html) --- ## PoL Bio-Image Analysis GPU Accelerated Image Analysis Training School Tags: Bioimage Analysis, Python, Include In Dalia Content type: Event, Notebook [https://biapol.github.io/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis/intro.html](https://biapol.github.io/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis/intro.html) --- ## PoL Bio-Image Analysis Training School on GPU-Accelerated Image Analysis Stephane Rigaud, Brian Northan, Till Korten, Neringa Jurenaite, Apurv Deepak Kulkarni, Peter Steinbach, Sebastian Starke, Johannes Soltwedel, Marvin Albert, Robert Haase Licensed CC-BY-4.0 This repository hosts notebooks, information and data for the GPU-Accelerated Image Analysis Track of the PoL Bio-Image Analysis Symposium. Tags: Gpu, Clesperanto, Dask, Python, Include In Dalia Content type: Notebook [https://github.com/BiAPoL/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis/](https://github.com/BiAPoL/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis/) --- ## Python Workshop - Image Processing Karin Sasaki, Jonas Hartmann Licensed UNKNOWN Tags: Python, Include In Dalia Content type: Code, Notebook [https://github.com/karinsasaki/python-workshop-image-processing](https://github.com/karinsasaki/python-workshop-image-processing) --- ## Python for Microscopists Sreenivas Bhattiprolu Licensed MIT Tags: Python, Bioimage Analysis, Include In Dalia Content type: Notebook, Collection [https://github.com/bnsreenu/python_for_microscopists](https://github.com/bnsreenu/python_for_microscopists) --- ## QI 2024 Analysis Lab Manual Beth Cimini, Florian Jug, QI 2024 Licensed CC-BY-4.0 This book contains the quantitative analysis labs for the QI CSHL course, 2024 Tags: Python, Include In Dalia Content type: Notebook [https://bethac07.github.io/qi_2024_analysis_lab_manual/intro.html](https://bethac07.github.io/qi_2024_analysis_lab_manual/intro.html) --- ## QM Course Lectures on Bio-Image Analysis with napari 2024 Marcelo Leomil Zoccoler Licensed CC-BY-4.0 In these lectures, we will explore ways to analyze microscopy images with Python and visualize them with napari, an nD viewer open-source software. The analysis will be done in Python mostly using the scikit-image, pyclesperanto and apoc libraries, via Jupyter notebooks. We will also explore some napari plugins as an interactive and convenient alternative way of performing these analysis, especially the napari-assistant, napari-apoc and napari-flim-phasor-plotter plugins. Tags: Napari, Python, Include In Dalia Content type: Notebook [https://zoccoler.github.io/QM_Course_Bio_Image_Analysis_with_napari_2024](https://zoccoler.github.io/QM_Course_Bio_Image_Analysis_with_napari_2024) --- ## QuPath for Python programmers Alan O'Callaghan, Léo Leplat Published 2024-10-23 Licensed UNKNOWN These are the notebooks and associated files for the i2k 2024 QuPath for Python programmers workshop. Tags: Python, Notebooks, Open Source Software, Bioimage Analysis, Include In Dalia Content type: Github Repository, Notebook, Collection [https://github.com/qupath/i2k-qupath-for-python-programmers](https://github.com/qupath/i2k-qupath-for-python-programmers) --- ## ZEN & Python workshop Licensed GPL-3.0 Tags: Python, Napari, Bioimage Analysis, Include In Dalia Content type: Collection, Notebook [https://github.com/zeissmicroscopy/ZEN_Python_OAD_workshop](https://github.com/zeissmicroscopy/ZEN_Python_OAD_workshop) --- ## ZeroCostDL4Mic: exploiting Google Colab to develop a free and open-source toolbox for Deep-Learning in microscopy Lucas von Chamier, Romain F. Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-pérez, Pieta Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L Jones, Loic Alain Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, Ricardo Henriques Licensed MIT Tags: Bioimage Analysis, Exclude From Dalia Content type: Notebook, Collection [https://github.com/HenriquesLab/ZeroCostDL4Mic](https://github.com/HenriquesLab/ZeroCostDL4Mic) [https://www.nature.com/articles/s41467-021-22518-0](https://www.nature.com/articles/s41467-021-22518-0) [https://doi.org/10.1038/s41467-021-22518-0](https://doi.org/10.1038/s41467-021-22518-0) --- ## imagequantification101 Virginie, Guillaume Witz, Joel Lüthi Published 2022-08-17T14:55:16+00:00 Licensed BSD-3-CLAUSE Tags: Bioimage Analysis, Include In Dalia Content type: Github Repository, Notebook, Collection [https://github.com/uhlmanngroup/imagequantification101](https://github.com/uhlmanngroup/imagequantification101) --- ## numpy pandas course Guillaume Witz Licensed BSD-3-CLAUSE Tags: Python, Include In Dalia Content type: Notebook [https://github.com/guiwitz/NumpyPandas_course](https://github.com/guiwitz/NumpyPandas_course) --- ## patho_prompt_injection JanClusmann, Tim Lenz Published 2024-11-08T08:32:03+00:00 Licensed GPL-3.0 Tags: Histopathology, Bioimage Analysis, Exclude From Dalia Content type: Github Repository, Notebook [https://github.com/KatherLab/patho_prompt_injection](https://github.com/KatherLab/patho_prompt_injection) --- ## shapeanalysis101 Virginie, Johannes Hugger Published 2021-05-17T13:32:40+00:00 Licensed BSD-3-CLAUSE A tutorial of classical shape analysis methods Tags: Bioimage Analysis, Include In Dalia Content type: Github Repository, Notebook, Collection [https://github.com/uhlmanngroup/shapeanalysis101](https://github.com/uhlmanngroup/shapeanalysis101) ---