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Zbigniew Mikulski
เข้าร่วมเมื่อ 9 พ.ค. 2015
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 th-cam.com/video/mVxNgKNTnWc/w-d-xo.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 object size
00:03:51 Creating pixel classifier for pancreatic islets
00:04:52 Tips for making a good classifier
00:06:41 Selecting objects by classification
00:07:21 Pixel classifier settings
00:07:40 Explanation of Scales
00:09:02 Dealing with artefacts
00:09:56 Question: why use the polyline tool?
00:11:20 The special case of Ignore* classes
00:12:09 Creating objects from pixel classifier
00:12:39 Duplicating image for a fresh start
00:13:21 Don't split your tissue but do split islets
00:14:12 Shift + F to fill annotations
00:15:08 Making peri-islet regions
00:16:52 Effect of removing interior
00:17:21 Effect of constraining to parent
00:18:23 Making an exocrine region
00:18:48 Making inverse annotation
00:19:14 Resolving overlapping regions
00:20:10 Merging islets
00:21:50 Use scripting to do more complex operations
00:22:46 Manual corrections
00:23:13 Tip for cell detections
00:23:30 Making use of object hierarchy
Please follow this document to get everything you need to fully participate in this training course (software, files, cheat sheets, and additional resources):
docs.google.com/document/d/1VyPtSbvnUC3EWnCVSRmFgFnhsXNHfOkAxOVyhkpYn8I
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-from-samples-to-knowledge-2023-is-available-online/88618
The more information you can include about your question, the more helpful our answers can be.
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 th-cam.com/video/mVxNgKNTnWc/w-d-xo.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 object size
00:03:51 Creating pixel classifier for pancreatic islets
00:04:52 Tips for making a good classifier
00:06:41 Selecting objects by classification
00:07:21 Pixel classifier settings
00:07:40 Explanation of Scales
00:09:02 Dealing with artefacts
00:09:56 Question: why use the polyline tool?
00:11:20 The special case of Ignore* classes
00:12:09 Creating objects from pixel classifier
00:12:39 Duplicating image for a fresh start
00:13:21 Don't split your tissue but do split islets
00:14:12 Shift + F to fill annotations
00:15:08 Making peri-islet regions
00:16:52 Effect of removing interior
00:17:21 Effect of constraining to parent
00:18:23 Making an exocrine region
00:18:48 Making inverse annotation
00:19:14 Resolving overlapping regions
00:20:10 Merging islets
00:21:50 Use scripting to do more complex operations
00:22:46 Manual corrections
00:23:13 Tip for cell detections
00:23:30 Making use of object hierarchy
Please follow this document to get everything you need to fully participate in this training course (software, files, cheat sheets, and additional resources):
docs.google.com/document/d/1VyPtSbvnUC3EWnCVSRmFgFnhsXNHfOkAxOVyhkpYn8I
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-from-samples-to-knowledge-2023-is-available-online/88618
The more information you can include about your question, the more helpful our answers can be.
มุมมอง: 81
วีดีโอ
Multiplex classifiers
มุมมอง 12014 วันที่ผ่านมา
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 ...
Subcellular detections
มุมมอง 181หลายเดือนก่อน
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...
Reproducibility
มุมมอง 124หลายเดือนก่อน
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 - ...
Advanced Scripting
มุมมอง 3637 หลายเดือนก่อน
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 ...
Review of Day 1
มุมมอง 3317 หลายเดือนก่อน
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...
Welcome to From Samples to Knowledge 2023: QuPath Training Course
มุมมอง 6857 หลายเดือนก่อน
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
Workflows and Scripts
มุมมอง 2347 หลายเดือนก่อน
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...
Introduction to QuPath
มุมมอง 2.1K7 หลายเดือนก่อน
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
มุมมอง 6287 หลายเดือนก่อน
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...
Density maps and Distances
มุมมอง 6797 หลายเดือนก่อน
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...
Where to get help?
มุมมอง 977 หลายเดือนก่อน
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...
InstanSeg
มุมมอง 2397 หลายเดือนก่อน
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...
Discussion on Quantification
มุมมอง 3497 หลายเดือนก่อน
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
มุมมอง 4627 หลายเดือนก่อน
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...
Artifacts: Avoiding and compensating for them
มุมมอง 3467 หลายเดือนก่อน
Artifacts: Avoiding and compensating for them
Image Analysis, AI, and QuPath - keynote by Pete Bankhead
มุมมอง 1.9K7 หลายเดือนก่อน
Image Analysis, AI, and QuPath - keynote by Pete Bankhead
From Samples to Knowledge 2023: QuPath training course
มุมมอง 8627 หลายเดือนก่อน
From Samples to Knowledge 2023: QuPath training course
Running a complex project in QuPath 0.3.2
มุมมอง 10K2 ปีที่แล้ว
Running a complex project in QuPath 0.3.2
Introduction to SketchUp for 3D printing
มุมมอง 913 ปีที่แล้ว
Introduction to SketchUp for 3D printing
How do you calculate the total number of spots estimated? When I do this, the value that shows up for me is NaN, and I have to use script to even display the estimated value. Thank you
Hi Alex, please ask your question on the image.sc forum: forum.image.sc/t/qupath-training-course-from-samples-to-knowledge-2023-is-available-online/88618/2 Thank you!
Thank you so much. I've been working with QuPath for two months, and I checked almost all the websites and TH-cam channels that I could find. However, this channel gave me the exact information I was looking for and helped me a lot. Thanks to you and the person who sent me your video on the forum :)
good video, but please could you talk bit clearer and not go so fast !! thank you
thanks for sharing. I am a big fan of Qupath and Pete.
Great software and resource, thanks
Hello , i need your email, thank you
pervert
Thank you
amazing
Great 👍 i am also seeking a phd position at scholarship.. in this field...i am currently working on histopathology images classification using deep learning.. i dont mind if u offer me a phd position... seeking seriously..
Great seminar! Thanks for your contribution!
What a wonderful seminar. Thank you to all speakers!
Its an amazing tool..i want to annotate an image in qupath and then want to get patches from labeled portions in separate folders and patches from norml image in separate folder...
Please make a short tutorial of making patches from svs file using qupath.,i want to perform tiling of huge sized .svs image...
amazing
It's amazing! Thanks a lot for uploading this
Glad you like it! If we get a bit more free time we will try to do a redo of exercises using version 0.2.1 - there is a chance it will be a bit less chaotic :D
Hi Guys, Thank you so much for posting this. Both days are so helpful. Great teaching. Thanks also to Pete for Qupath.
Glad it was helpful! If you have any questions tag us on forum.image.sc :)