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Laura Nicolas-Saenz
เข้าร่วมเมื่อ 12 ก.พ. 2024
Intro to scripting in QuPath
🚀 Welcome to the latest episode of "From Zero to QuPath Hero"! 🎉 In this instalment, join me while I show the different things you can do using scripts, following qupath.readthedocs.io/en/stable/docs/scripting/overview.html and using images from: openslide.cs.cmu.edu/download...
🖥️✨ Don't miss out-watch now and level up your QuPath skills! #QuPathScripting #ImageAnalysis #WorkflowAutomation #Tutorial 📽️✨
🖥️✨ Don't miss out-watch now and level up your QuPath skills! #QuPathScripting #ImageAnalysis #WorkflowAutomation #Tutorial 📽️✨
มุมมอง: 360
วีดีโอ
Creating pipelines and workflows with QuPath
มุมมอง 3715 หลายเดือนก่อน
🚀 Welcome to the latest episode of "From Zero to QuPath Hero"! 🎉 In this instalment, join me while I go through a whole image analysis pipeline and learn how to create workflows and scripts: qupath.readthedocs.io/en/stable/docs/scripting/index.html and using images from: openslide.cs.cmu.edu/download... 🖥️✨ Discover how to automate workflows and convert them into scripts to streamline your imag...
Superpixels and QuPath
มุมมอง 3776 หลายเดือนก่อน
🚀 Welcome to the latest episode of "From Zero to QuPath Hero"! 🎉 In this installment, join me while I learn how to work with superpixels in QuPath following this tutorial: qupath.readthedocs.io/en/stable/docs/tutorials/superpixels.html and using images from: openslide.cs.cmu.edu/download... In this video, I delve into the process of creating 3 different types of superpixles/tiles, training pixe...
Pixel classification with QuPath
มุมมอง 6486 หลายเดือนก่อน
🚀 Welcome to the latest episode of "From Zero to QuPath Hero"! 🎉 In this installment, join me on a journey through the intricacies of pixel classification in QuPath following this tutorial: qupath.readthedocs.io/en/stable/docs/tutorials/pixel_classification.html and using images from: openslide.cs.cmu.edu/download... In this video, I delve into the process of training pixel classifiers, refinin...
How to do Multiplexed Analysis using Qupath
มุมมอง 1.2K6 หลายเดือนก่อน
Hello future QuPath heroes! In this video I learn how to do cell detection, map creation, object classification, and classifier merging for multiplex images! We follow this tutorials: qupath.readthedocs.io/en/stable/docs/tutorials/cell_classification.ht The image used in this video can be found in : downloads.openmicroscopy.org/images/Vectra-QPTIFF/perkinelmer/PKI_fields/ (LuCa-7color_[13860,52...
Exporting Measurements with QuPath
มุมมอง 7046 หลายเดือนก่อน
In this video, I show you how to export your measurements after image analysis with QuPath. We will follow the docs: qupath.readthedocs.io/en/stable/docs/tutorials/exporting_measurements.html for this. We learn the easy and the propper way to do it and see how these measurements look. The images used in this video can be found in : openslide.cs.cmu.edu/download... And Pete's answering videos ca...
Cell Classification and Density Maps with QuPath
มุมมอง 9336 หลายเดือนก่อน
Hello future QuPath heroes! In this video I learn how to do cell detection, map creation, smoother maps, area classification, intensity thresholding and density maps! We follow 2 tutorials this time, this: qupath.readthedocs.io/en/stable/docs/tutorials/cell_classification.html and this: qupath.readthedocs.io/en/stable/docs/tutorials/density_maps.html The images used in this video can be found i...
Detecting (Positive) Cells with QuPath
มุมมอง 1.7K6 หลายเดือนก่อน
In this video, I show you how to separate stains in different types of images using QuPath. We will follow the docs: qupath.readthedocs.io/en/stable/docs/tutorials/cell_detection.html. for this. We will learn the difference between normal and positive cell detection, converting the cells to point annotations, and what to do when you mess up. The images used in this video can be found in : opens...
Detecting Tissue with QuPath
มุมมอง 1.2K6 หลายเดือนก่อน
In this video, I show you how to separate stains in different types of images using QuPath. We will follow the docs: qupath.readthedocs.io/en/stable/docs/tutorials/thresholding.html for this. We will learn how to create objects using manual annotations, how to create and save thresholders, and how to apply them to other images The images used in this video can be found in : openslide.cs.cmu.edu...
Separating Stains in QuPath
มุมมอง 1.9K6 หลายเดือนก่อน
In this video, I show you how to separate stains in different types of images using QuPath. We will follow the docs: qupath.readthedocs.io/en/stable/docs/tutorials/separating_stains.html for this. We will learn about colour deconvolution, working with stain vectors, and viewing the scatter plots that represent our stains. You'll also hearm me complain about ICC profiles. The images used in this...
Viewing images with QuPath
มุมมอง 2.3K7 หลายเดือนก่อน
In this video, I show you how to view images using QuPath. We will follow the docs: qupath.readthedocs.io/en/stable/docs/starting/index.html to learn how to import images, navigate them, visualize more than one at the same time, create projects, set the image types, and more! The images used in this video can be found in : openslide.cs.cmu.edu/download/openslide-testdata/
How to Install QuPath
มุมมอง 1.4K7 หลายเดือนก่อน
In this short video, we learn how to install and run QuPath. Download link: qupath.github.io/
From Zero to QuPath Hero: Introduction
มุมมอง 3.3K7 หลายเดือนก่อน
The hero's journey is the common template of stories that involve a hero who goes on an adventure, is victorious in a decisive crisis, and comes home changed or transformed. In this series of videos, we will embark on our own journey to become masters of QuPath from the very basics to the most complex of tasks. If you have ever felt frustrated or a little bit stupid when learning a new skill, c...
These videos are great! I have to learn QuPath for my work, and this is very very helpful!!!
Thank you for the review...I am trying to quantitate adipose tissue in bone marrow vs. cellularity...appreciate if you can guide how to annotate adipose tissue (empty space) vs. cellular areas.
Nice! so i would love to integrate AI into this software and would love to collaborate with you.
Can this method be used to detect fluorescent cells in 3D images of mouse brain?
Hello, I would appreciate an answer 😊 What are the system requirements of a laptop to run the software smoothly? I would appreciate a reference in terms of memory, processor, cpu and graphic card, I did not find on the net current data for 2024 version 5.1 Thanks 
Nice walkthrough! Can you explain how the H&E images differ? Are they the same slide from different scanners? Or different scanner settings?
great channel. what are you using for downstream analysis R studio or as you mentioned matlab or python. can you make a video on an analysis workflow? thanks for the useful videos!
Hi. Thank you for the video. Here we "estimate stain vectors" for one image and then apply it with the script to others in the project. What if the other images are not suitable for the new values? Does the script apply results based on this script generated image or it calculates on that new image separately?
Hi! If you have selected actual values for the stain vectors, those will be applied to the other images. Indeed you can only do this if you know your images are very very similar and there is no variation in colour profiles or staining. Certainly a step that might be better to do manually for each image if you have a manageable number of them.
@@lanicolassathank you. If possible, I would like to annotate each image with areas (or select whole image) to estimate stain vectors, and then let the "auto" adjust to be applied to all images separately.
Hi firstly, thank you so much for informative videos, I dont have a option of set grid, i HAVE A OPTION " RESET GRID SIZE" WHEN i AM CLICKING ON IT, ITS OPENING NOTHING. can you please help me
Hi Laura! I uploaded a short video explaining the confusing behaviour with the PDL1 classifiers: th-cam.com/video/4YXbNNsTnow/w-d-xo.html
Good point, expecting export type 'Image' to export an image seems reasonable :) Any ideas for a less confusing label to use for the option (i.e. export a summary of everything)?
export level? or maybe it would be less confusing if ºIºmage wasn't the default option
Hey Laura! Here's my explanation for why the 'set cell classification' thing annoyingly blocks your image interactions: th-cam.com/video/lwq2jbsghJ4/w-d-xo.html
Hi Laura! Since I kinda created the frustrations, I've posted a reply showing 5 ways to get rid of detections after the annotation has gone (and some other tips/info): th-cam.com/video/zFTnfv_XWg4/w-d-xo.html
Hi, just my two cents: 1:16 brown stains are in fact melanin pigment produced by melaocytes and engulfed by keratinocytes. So they are the natural elements of this biopsy. 1:22 the green is artifical, we ink the surgical margins with tissue dyes or commercial indian ink. they are used to identify if there is remaining tissue at the surgical margin. They can be in value to assess automatic surgical margin evaluation.
That is super interesting and helpful! I'll be sure to include that info next time I find that in an image. Thank you!!!!!!
Can one open multiple images side by side while inside a project?
Absolutely! Just set the grid size to whatever you need, click on one of the multiview windows to select it and then double-click on one of the images of your project. Repeat for as many windows as you have and you'll be able to have multiple images open while inside a project. :)
@@LauraNicolasSaenz thank you, I had to double click the area first and then click on the image