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#1StarDist - Object Detection with Star-convex Shapes - GitHub
This repository contains the Python implementation of star-convex object detection for 2D and 3D images, as described in the papers: Uwe Schmidt, Martin Weigert ...
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#2StarDist - GitHub
simple package for augmentation of n-dimensional arrays. Python 26 4 ...
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#3stardist · GitHub Topics
script to create labels (for training a deep neural network) based on ...
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#4QuPath extension to run StarDist nucleus detection
Welcome to the StarDist extension for QuPath! This adds support for running the ...
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#5StarDist ImageJ/Fiji plugin - GitHub
This is the ImageJ/Fiji plugin for StarDist, which can be used to apply already trained models to new images. Note: The plugin (currently) only supports 2D ...
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#6StarDist napari plugin - GitHub
StarDist has originally been developed (see papers) for the segmentation of densely packed cell nuclei in challenging images with low signal-to-noise ratios.
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#7MarkZaidi/Universal-StarDist-for-QuPath - GitHub
Transfer trained StarDist models across imaging modalities - GitHub ...
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#8ASHISRAVINDRAN/stardist_pytorch: StarDist PyTorch - GitHub
Cell Detection with Star-convex Polygons: PyTorch implementation.
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#9StarDist - ImageJ Wiki
This is the ImageJ/Fiji plugin for StarDist, a cell/nuclei detection method for microscopy images with star-convex shape priors. The plugin can be used to ...
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#10stardist_example_2D_colab.ipynb - Colaboratory
To run the workflow on your own workstation/data, consider using our jupyter notebooks: https://github.com/stardist/stardist/tree/master/examples.
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#11FAQs for StarDist - Object Detection with Star-Convex ...
FAQs for StarDist - Object Detection with Star-Convex Polygons¶. https://github.com/stardist/stardist/raw/master/. This page provides answers to frequently ...
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#12StarDist — QuPath 0.4.3 documentation - Read the Docs
See the original StarDist papers and GitHub repos for information about training your own models. Tip. The he_heavy_augment model is capable of more than one ...
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#13An introduction to object segmentation using StarDist library in ...
For details on installing StarDist library and other examples:https:// github.com/ stardist /stardistStardist helps with object detection of ...
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#14plugin | napari-merge-stardist-masks by Niklas Netter
Segment non-star-convex objects with StarDist by merging masks. ... pip install git+https://github.com/gatoniel/napari-merge-stardist-masks.git ...
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#15How to use the stardist.models.StarDist3D function in ... - Snyk
Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately. Enable here. github mpicbg-csbd / stardist / tests / test_model3D.
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#16stardist | napari plugin Alfa Cohort
stardist. Contributor(s): Uwe Schmidt (@uschmidt83), Martin Weigert (@maweigert); References: Github, Publications. Purpose. Describe the problem you are ...
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#17Baseline And Tutorial - Grand Challenge
Stardist : https://github.com/stardist/stardist; Omnipose: https://github.com/kevinjohncutler/omnipose. This nuclear segmentation summary paper is also very ...
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#18StarDist Image Segmentation Improves Circulating ... - NCBI
In 442 blood samples from cancer patients, StarDist segmented 99.95% of CTC segmented by CellSearch, ... The StarDist method from github ...
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#193D Stardist: no detection on inference - Image.sc Forum
Hi, I'm having some trouble with a 3D Stardist model I'm trying to ... lru_cache # https://github.com/stardist/stardist/issues/107 class ...
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#20Uwe Schmidt on Twitter: "Bonus: You can now export 2D ...
We just revamped our StarDist code to now cover both 2D and 3D versions, including detailed example notebooks. Code: https://github.com/mpicbg-csbd/stardist ...
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#21Using StarDist in arivis Vision4D
StarDist is a deep learning-based method for 2D and 3D nucleus detection, developed & published by Martin Weigert and Uwe Schmidt: github.com/stardist/.
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#22StarDist2D Nucleus Segmentation - Public Modules - APEER
StarDist 2D Cell Nucleus Segmentation based on star-convex object ... information can be found project repository: GitHub - StarDist.
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#23Course Data Analysis - Cellular Imaging
For this course we will use QuPath 0.3.0, Fiji (+Stardist Plugin) and Ilastik ... (https://github.com/qupath/qupath-extension-stardist).
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#24StarDist - RMS
... provided plugins for other common image analysis software suites (e.g., Fiji, napari, QuPath). https://github.com/mpicbg-csbd/stardist.
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#25Nuclei instance segmentation and classification ... - arXiv Vanity
Based on our own augmentation library Augmend, 2 2 2https://github.com/stardist/augmend 2 we apply common geometric augmentations (flips and 90 degree rotations, ...
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#26Stardist Segmentation in Fiji - WWU Confluence Wiki
Stardist Github : ... https://nbviewer.org/github/stardist/stardist/tree/master/ ... Fiji - Macro for Batch segmentation using Stardist.
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#27BioImage.IO
... ilastik, ImJoy and more; Try model instantly with BioEngine; Contribute your models via Github ... StarDist - Object Detection with Star-convex Shapes.
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#28Star-convex Polyhedra for 3D Object Detection and ...
datasets that our approach (STARDIST-3D) leads to supe- ... documentation is available at https://github.com/ mpicbg-csbd/stardist.
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#29'StarDist2D' object has no attribute '_tile_overlap' - Lightrun
See original GitHub issue ... AttributeError Traceback (most recent call last) /usr/local/lib/python3.6/dist-packages/stardist/models/base.py in ...
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#30Nuclei instance segmentation and classification in ...
We show that StarDist, a deep learning nuclei segmentation method originally developed for fluorescence microscopy, can be extended and ...
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#31StarDist - ImageJ - BIII
This is the ImageJ/Fiji plugin for StarDist, a cell/nuclei detection method for microscopy images with star-convex shape priors ( typically for Dapi like ...
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#32Uwe Schmidt (@[email protected])
If you're interested in the details of our #StarDist-based ... stardist/examples/conic-2022 at conic-2022 · stardist/stardistGitHub.
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#33quantify-nucleus 0.0.2 on PyPI - Libraries.io
This package uses stardist(https://github.com/stardist/stardist) for segmentation and napari(https://github.com/napari/napari) for ...
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#34Image-segmentation networks (U-Net and StarDist) a, b ...
Image-segmentation networks (U-Net and StarDist) a, b Example of data ... and https://github.com/utraf-pasteur-institute/CellWalker-blender ) under a GPL-3 ...
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#35Scellseg: A style-aware deep learning tool for adaptive cell ...
other models, U-Net2, U-Net3, StarDist,24 HoVer,25 and Cellpose (see STAR ... For StarDist, the loss function refers to https://github.
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#36Stardist - :: Anaconda.org
StarDist. copied from cf-staging / stardist ... License: MIT; Home: https://github.com/stardist/stardist ... conda install -c conda-forge stardist ...
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#37ReadImageJROI - File Exchange - MATLAB Central
To view or report issues in this GitHub add-on, visit the GitHub ... Worked nicely with zip files of ROIs generated using an ImageJ plugin StarDist.
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#38gatoniel/merge-stardist-masks: v0.1.2 | Zenodo
gatoniel/merge-stardist-masks: v0.1.2 ·.cookiecutter.json 387 Bytes ·.darglint 29 Bytes ·.flake8 263 Bytes ·.gitattributes 19 Bytes ·.github.
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#39StarDist 2D – KNIME Community Hub
This component uses StarDist for segmentation of convex-shaped objects. ... plugin available at https://github.com/stardist/stardist-imagej.
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#40notebook: segmenting nuclei with the stardist napari plugin
The data were downloaded from the OpticalPooledScreens github repository. Loading the data#. We will start by loading an image of DAPI stained nuclei. We can ...
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#41REDPOL-open - Nicolas Elie - GitLab Unicaen
ipynb. This program is directly from an example provided on the github Stardist repository. jupyter nbconvert --execute --clear-output ...
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#42StarDist: Application of the deep-learning tool for phase ...
Although being a recent deep-learning tool, StarDist has much documentation and ... in the GitHub page and many threads in forum.image.sc.
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#43Scientific Computing / bioimage_team / stardist_nnet_explore
These notebooks are based on the stardist pip version from 2019-12. ... stardist (Myers lab) repository: https://github.com/mpicbg-csbd/ ...
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#44SplineDist: Automated Cell Segmentation with Spline Curves
We use the high-quality StarDist codebase ( github.com/mpicbg-csbd/stardist ) and mainly modify modules associated with ground truth generation ...
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#45[2203.02284] Nuclei instance segmentation and classification ...
Abstract: Instance segmentation and classification of nuclei is an important task in computational pathology. We show that StarDist, ...
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#46Omnipose: a high-precision morphology-independent solution ...
Cellpose and StarDist outperform Mask R-CNN and MiSiC at high IoU ... from the Wormpose GitHub (https://github.com/iteal/wormpose_data) ...
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#47TSFD-Net: Tissue specific feature distillation network for nuclei ...
The code is available at: https://github.com/Mr-TalhaIlyas/TSFD. ... However, for a set of pre-defined directions, StarDIST (Schmidt et al., 2018) predicts ...
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#48Document History - c4science
... the latest version of QuPath from https://qupath.github.io/ ==1.1. ... https://github.com/qupath/qupath-extension-stardist | StarDist ...
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#49Fluorescence lifetime image microscopy prediction with ...
S2A) (34, 35), and Stardist (Supplementary Material Appendix Fig. ... https://github.com/qubvel/segmentation_models) was used for training with the Adam ...
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#50Nuclei segmentation and classification in histopathology ...
Here we describe how we used StarDist, a deep learning based approach based on star-convex shape representations, for the Colon Nuclei ...
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#51Cellpose: a generalist algorithm for cellular segmentation
4 : Example Stardist segmentations. ... Schmidt, U. & Weigert, M. StarDist—object detection with star-convex shapes (GitHub, ...
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#52stardist-napari - Wheelodex
METADATA ; Author: Uwe Schmidt, Martin Weigert ; Author-Email: research[at]uweschmidt.org, martin.weigert[at]epfl.ch ; Home-Page: https://github.
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#53STARDIST: DETECCIÓN DE OBJETOS EN IMÁGENES ...
Hoy os queremos hablar de otra herramienta (StarDist) que utiliza ... en la página de StarDist (https://github.com/mpicbg-csbd/stardist) ...
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#54Arivis Vision4D Application: StarDist - SANE ASIA
Image Source: https://github.com/stardist/stardist. Arivis AG has recently published a detailed protocol on performing StarDist segmentation directly in ...
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#55Automated cell tracking using StarDist and TrackMate
The ability of cells to migrate is a fundamental physiological process involved in embryonic development, tissue homeostasis, immune surveillance, and wound ...
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#56Cell Detection with Star-convex Polygons - uweschmidt.org
StarDist achieves higher AP than all other compared ... StarDist can be trained to do shape completion for ... https://github.com/mpicbg-csbd/stardist.
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#57Embedding-based Instance Segmentation in Microscopy
Mask R-CNN (He et al., 2017) or StarDist (Schmidt et al., 2018), for example, avoid mul- ... Data download links can be found on GitHub as well.
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#58stardist/stardist_impl/predict_stardist_2d.py · master · Bio-IT ...
... see # https://github.com/hci-unihd/batchlib/blob/master/batchlib/segmentation/stardist_prediction.py def run_prediction(image_files, ...
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#59FastPathology: An Open-Source Platform for Deep Learning ...
https://github.com/SINTEFMedtek/FAST-Pathology/. INDEX TERMS Deep learning, neural networks, ... made through StarDist [20], using TensorFlow to deploy a.
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#60Live Cell Analysis - StarDist Segmentation - Figshare
Fiji/ImageJ macro for analysis of live cell imaging data of mouse B cells. Macro was developed by Cameron J Nowell of Monash University (cameron ...
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#61How to solve assertion error in Google Colab? - Stack Overflow
Screenshot of the code from Stardist github page. Here is my attempt at reconstructing the code with the error I get when I attempt to run ...
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#62StarDist Image Segmentation Improves Circulating Tumor Cell ...
Stardist Segmentation. The StarDist method from github (https://github.com/stardist/stardist, accessed on 1 June 2021) was applied with a few non ...
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#63CellSeg: a robust, pre-trained nucleus segmentation and pixel ...
For StarDist, brightfield and fluorescence images were segmented ... and use CellSeg (https://michaellee1.github.io/CellSegSite/index.html).
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#64ImageJ实用教程——DeepImageJ（插件篇） - 知乎专栏
deepImageJ • Home deepimagej.github.io/deepimagej/index.html ... 好的模型，就可以将该模型运用在自己的图像处理任务中。这与之前文章提到的StarDist，原理相同：.
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#65PyTorch Hub
PyTorch Hub supports publishing pre-trained models (model definitions and pre-trained weights) to a GitHub repository by adding a simple hubconf.py file.
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#66Detection and segmentation of morphologically complex ...
Additionally, we compare the performance to Stardist [12], ... and models are available at https://github.com/umr-ds/feature_pyramid_fusion.
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#67MultiStar: Instance Segmentation of Overlapping Objects with ...
This allows us to apply the ideas of StarDist to images ... Review of StarDist ... https://github.com/hci-unihd/MultiStar.
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#68BlastoSPIM Models
Performance results on moderate SNR Images per developmental stage for both the Stardist-3D early embryo model and the Stardist-3D late blastocyst model. This ...
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#69Automated cell tracking using StarDist and TrackMate [version 1
pipeline illustrating how the deep learning network StarDist can be ... Source code available from: https://github.com/HenriquesLab/.
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#70StarDistについて - Qiita
StarDist とは，星型凸多角形(Star-convex)を用いた細胞核のセグメンテーションを行うための手法です． StarDistはGithubにて論文やコードがまとめられて ...
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#71NEUBIAS Academy-Webinars-Archive-Spring2020
This will be a live demo and discussion of StarDist. The Webinar will be broadcasted live with Zoom, in the form of an interactive webinar with ...
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#72Open-source deep-learning software for bioimage segmentation
These web apps include several for light microscopy: StarDist ... In such cases, GitHub repositories or the Scientific Community Image Forum ...
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#73Qupath-extension-stardist Alternatives and Reviews (2023)
Which is the best alternative to qupath-extension-stardist? ... models with your specific images. github.com/BIOP/qupath-extension-cellpose ...
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#74Troubleshooting - pr4deepr/GutAnalysisToolbox GitHub Wiki
It works fine on a Mac OS with Intel chips as far as we know. Out of memory errors. When running StarDist on really large images or if your ...
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#75Stardistscenario - CSBDeep
Authorship This example is part of the Stardist - Object Detection with Star-convex Shapes described in the papers: Cell Detection with Star-convex ...
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#76Radiation Oncology and Radiotherapy Part B
Additional information can be found in the StarDist Github repository (https://github.com/mpicbg-csbd/stardist). After cell segmentation, a list of several ...
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#77Medical Image Computing and Computer Assisted Intervention – ...
For StarDist, we calculate the optimal number of rays on the training data, ... but the representations https://github.com/stardist/stardist.
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#78Proceedings of the 2021 Indiana O’Brien Center Microscopy ...
... plugin Plugin Inference with StarDist Inference in ImageJ with BioImage. ... and CellAnalyst StarDist https: //github.com/stardist/stardist HistomicsML2 ...
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#79Deep Generative Models: Second MICCAI Workshop, DGM4MICCAI ...
Schmidt, U., Weigert, M.: Stardist (2022). https://github.com/stardist/stardist 24. Schmidt, U., Weigert, M., Broaddus, C., Myers, G.: Cell detection with ...
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#80pix2pix - Korea
... !pip install git+https://github.com/tensorflow/examples.git from … ... care , unet , noise2void , stardist , zerocostdl4mic , cyclegan ...
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#81Fiji: ImageJ, with "Batteries Included"
Like ImageJ itself, Fiji is an open source project hosted on GitHub, developed and written by the community. Plugins. Fiji features thousands of plugins that ...
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