Видео 36
Просмотров 53 346

21:45

Subcellular detections

16:35

Cell Detection and Cell Measurements

54:46

ROI Manipulation

Sara McArdle presents different ways of changing ROIs, and demonstrates how to create regions around pancreatic islets.
Files drive.google.com/drive/folders/1T9g4ex3TFVVCkZ7PdPl9w_61ySakUndI and a related presentation docs.google.com/presentation/d/1mvlVU4DazeDC3O_1GUL7MQUStqpwEDs8 are available for download.
00:00:00 Sara McArdle introduces ROI manipulation tools
00:00:25 Example: ROIs around tumors
see ruclips.net/video/mVxNgKNTnWc/видео.htmlsi=YUuYMBpJuvXoeWgu&t=5260
00:00:42 Example: ROIs around vessels
00:01:00 Human pancreas anatomy
00:01:48 Changing maximum display range
00:01:58 Finding tissue outline with a thresholder
00:03:13 Loading classifier and creating objects
00:03:36 Minimum ob...

Видео

21:45

Multiplex classifiers

Просмотров 6074 месяца назад

Sara McArdle shows how to extend object classifiers to multiplex imaging, demonstrating the built-in QuPath features to make this workflow straightforward and reproducible. Image files are here: drive.google.com/drive/folders/1T9g4ex3TFVVCkZ7PdPl9w_61ySakUndI 00:00:30 Making duplicate channel training images 00:01:48 Pro tip: do all of your measurements before creating training images 00:02:17 ...

16:35

Subcellular detections

Просмотров 4465 месяцев назад

Subcellular detections in QuPath are a convenient way of analyzing in-situ hybridization data. Sara McArdle explains how to use them for the analysis of RNAscope data. 00:00:00 Sara McArdle explains how to use subcellular detections in QuPath 00:04:26 Subcellular detections 00:03:39 Creating full image annotation and detecting cells 00:04:55 Setting up detection thresholds 00:06:16 Adjusting de...

12:37

Reproducibility

Просмотров 2005 месяцев назад

Mike Nelson discusses reproducibility in image analysis. The presentation with clickable links is available for download: docs.google.com/presentation/d/1fpUEmksUnyt52AQ6kM4wTtvjqQBshGM1/edit?usp=sharing&ouid=100186518387332557471&rtpof=true&sd=true 00:20 - Different levels of reproducibility 01:35 - Diverse evidence for lack of reproducibility 02:30 - Underreporting of imaging methods 04:40 - ...

52:13

Advanced Scripting

Просмотров 53111 месяцев назад

Sara McArdle details creating custom Groovy scripts for QuPath using 3 common example problems. This video is aimed at people who have done at least a bit of scripting in the past. Groovy files can be found here: github.com/saramcardle/Image-Analysis-Scripts/tree/master/QuPath Groovy Scripts/QuPath 0.5.0 and image files are here: drive.google.com/drive/folders/1T9g4ex3TFVVCkZ7PdPl9w_61ySakUndI ...

45:06

Review of Day 1

Просмотров 51711 месяцев назад

Review of lessons from Day 1, by Sara McArdle. Quickly reviews visualization options, cell detection, and classification. Please see previous videos for detailed explanations. Files drive.google.com/drive/folders/1T9g4ex3TFVVCkZ7PdPl9w_61ySakUndI and a related presentation docs.google.com/presentation/d/112oXGIPwoIAJAjaHkabE0pif7l24I0EM are available for download. 00:00 Overview and review of D...

54:46

Cell Detection and Cell Measurements

Просмотров 3 тыс.11 месяцев назад

Cell Detection and Cell Measurements

Welcome to From Samples to Knowledge 2023: QuPath Training Course

2:11

Welcome to From Samples to Knowledge 2023: QuPath Training Course

Просмотров 1 тыс.11 месяцев назад

A warm welcome from Sara McArdle, Mike Nelson, and Zbigniew Mikulski to FS2K 2023! Please follow this document to get everything you need: docs.google.com/document/d/1VyPtSbvnUC3EWnCVSRmFgFnhsXNHfOkAxOVyhkpYn8I

21:19

Workflows and Scripts

Просмотров 37511 месяцев назад

Zbigniew Mikulski shows how to use the Workflow Tab to apply the same analysis methods to multiple images, saving you time and reducing errors. Files drive.google.com/drive/folders/1T9g4ex3TFVVCkZ7PdPl9w_61ySakUnd and a related presentation docs.google.com/presentation/d/1ohQWIcol_I_FAfrRqHfWIkdmIX0xFYMa are available for download. 0:00 Creating Scripts for batching by Zbigniew Mikulski 0:10 Va...

1:04:06

Introduction to QuPath

Просмотров 4,3 тыс.11 месяцев назад

Introduction to QuPath by Mike Nelson, covering the major concepts and tools in QuPath and demonstrating a quick project (don’t worry, each step will be shown slower in later videos). Files drive.google.com/drive/folders/1T9g4ex3TFVVCkZ7PdPl9w_61ySakUndI and a related presentation docs.google.com/presentation/d/12M0pzIcM6ftcD6zn1TpndSCnbnC9t1XU are available for download. 0:00 Welcome by Zbigni...

QuPath Concepts: Pixels, Objects, and Classifiers

30:54

QuPath Concepts: Pixels, Objects, and Classifiers

Просмотров 1,2 тыс.11 месяцев назад

Pete Bankhead discusses what are Pixels, Objects, and Classifiers and how they are used in QuPath. 0:00 QuPath Concepts: Pixels, Objects, and classifiers by Pete Bankhead 1:31 Digital Image Analysis 6:41 Pathology Images are Big 8:27 Reduce the number of numbers 10:34 What's an object 14:06 Annotations vs detections 18:49 Simplify Shape to remove vertices 21:58 Cells, Tiles, and TMA Cores 22:57...

17:51

Density maps and Distances

Просмотров 1,1 тыс.11 месяцев назад

Sara McArdle shows how to use density maps in QuPath for spatial analysis. Files drive.google.com/drive/folders/1T9g4ex3TFVVCkZ7PdPl9w_61ySakUndI and a related presentation docs.google.com/presentation/d/1sqB1usAnFW8GrFADzFujwAV0aMy3ShOs are available for download. 01:13 Loading object classifier and applying classification 02:05 Density maps 03:29 Changing density maps visualization 05:46 Savi...

29:42

Where to get help?

Просмотров 15711 месяцев назад

Mike Nelson presents a plethora of useful resources and discusses how to get help with your image analysis problems. You can view or download the presentation with clickable links here: docs.google.com/presentation/d/1KFfFFEVrMLtF9FKujtgEMAA08tBP0rkH If you have any questions about the videos or the training course, please ask on this image.sc forum post. forum.image.sc/t/qupath-training-course...

16:37

InstanSeg

Просмотров 47911 месяцев назад

Thibaut Goldsborough reviews the Stardist and Cellpose algorithm and for the first time presents his novel method, InstanSeg. 0:00 Advanced Segmentation Methods by Thibaut Golds 0:46 Cellpose for complex shapes 5:08 When is Cellpose worth it? 7:16 PyTorch and TorchScript 9:27 Introducing InstanSeg, a novel segmentation algorithm! 12:03 Comparing 4 segmentation methods 13:17 InstanSeg works quic...

5:57

Discussion on Quantification

Просмотров 51411 месяцев назад

Sara McArdle, Mike Nelson, and Zbigniew Mikulski discuss the need for image quantification and highlight some approaches to extracting biological information from images, and presenting it in a numerical format that is easier to understand by other scientists. If you have any questions about the videos or the training course, please ask on this image.sc forum post. forum.image.sc/t/qupath-train...

Practical applications of multiplex analysis in QuPath

18:06

Practical applications of multiplex analysis in QuPath

Просмотров 66711 месяцев назад

Mark Zaidi presents how QuPath tools can be used in complex multiplex analysis for quantifying immune cell phenotypes in acute kidney injury. 00:00 Practical applications of QuPath analysis by Mark Zaidi 01:44 Acute Kidney Injury 02:37 Imaging Mass Cytometry 03:07 Cell segmentation with StarDist 04:34 Cell classification 04:56 Pixel classifier for renal structure segmentation 05:36 Spatial feat...