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Craig Daly
United Kingdom
เข้าร่วมเมื่อ 23 ก.ย. 2013
Image processing and analysis tutorials coupled with 3D animations for learning and teaching in physiology. Much of the content is aimed at undergraduate and postgraduate university students but some videos will be of more general interest. Some videos were created by project students as part of their Masters in Medical Visualisation. All of the 3D animations will include some element of real structural data collected using 3D laser scanning microscopy. 3D Modelling is used only to provide a spatial context. The goal is to build a library of anatomically accurate animations of various physiological processes.
Ilastik plugin for Fiji/ImageJ
Using Ilastik for machine learning with Fiji/ImageJ. A brief introduction and tutorial. **Erratum to avoid confusion - pixel classification uses a Random Forest - so strictly speaking not a NN - but that is available in other Ilastik options **.
มุมมอง: 6 376
วีดีโอ
Science & The Metaverse
มุมมอง 209ปีที่แล้ว
A brief introduction to the Metaverse and how Life Scientists (and/or microscope users) might take advantage of the promised digital landscape. Produced for the Glasgow Science Festival (June 2023). Part of the online 'Science on the sofa' section.
ChatGPT: Can it write ImageJ Macros?
มุมมอง 4.3Kปีที่แล้ว
A first look at ChatGPT. Is it a game changer for Image Analysis? Can it write an ImageJ Macro? If you cant get on to ChatGPT right now (cos its too busy) then this video might help.
Separate touching objects in ImageJ/Fiji (Watershed)
มุมมอง 10Kปีที่แล้ว
Quick ImageJ/Fiji tutorial on using watershed and analyse particles to extract touching objects.
Electron Microscope volume rendered in Autodesk Maya
มุมมอง 4092 ปีที่แล้ว
A block of 600 EM slices segmented in Slicer3D then rendered in Autodesk Maya. Part 1 shows the data. Part 2 will describe the image processing
Review and first reaction to Imaris 9.9.0
มุมมอง 2.2K2 ปีที่แล้ว
A short review and first impression of Imaris 9.9.0 Image Processing and Analysis Software.
Using different PSFs for Deconvolution (ImageJ/Fiji)
มุมมอง 2.9K2 ปีที่แล้ว
How to generate and apply different Point Spread Functions for use with DeconvolutionLab2 in ImageJ or Fiji - Short Tutorial
Fixing blurry images in Fiji/ImageJ (Deconvolution Lab2 plugin)
มุมมอง 9K2 ปีที่แล้ว
A quick and easy way to try out different deconvolution routines in imageJ or Fiji. A quick guide to getting started. Time markers below; 0 -1min Intro 1.01 - Intro Video 1.17 - Data Prep 2.54 - Running the plugin 3.37 - Point Spread Functions 5.00 - Regularized Inverse Filter 5.52 - Iterative Constrained Tikhonov Miller 10.20 - Richardson Lucy 13.00 - Round up
Trainable Weka Segmentation (Fiji Tutorial)
มุมมอง 13K2 ปีที่แล้ว
First steps to training a ML algorithm using Weka Segmentation in Fiji
Cell: The Genesis - VR Game Trailer
มุมมอง 5322 ปีที่แล้ว
Finally, it's here. A VR Cell physiology game funded by the Physiological Society. Developed by Craig Daly and Angela Douglass. You can download it from Itch.Io genesis-cell.itch.io/cell-the-genesis-vr
Getting started with macros in ImageJ
มุมมอง 17K2 ปีที่แล้ว
A very quick simple guide to creating macros in ImageJ
Shape Based Object Extraction in ImageJ or Fiji
มุมมอง 14K3 ปีที่แล้ว
using thresholding, shape descriptors and binary arithmetic to extract objects in ImageJ (or Fiji)
Virtual Reality (VR) for Research and teaching - Chatting with Edify VR
มุมมอง 5983 ปีที่แล้ว
A presentation (first 25 minutes) on my 40 year journey to VR for teaching and research. Chatting with the makers of the Edify platform; www.edify.ac/ and others for the remaining 30 minutes.
Image Arithmetic (Add & Subtract) using ImageJ
มุมมอง 16K3 ปีที่แล้ว
Quick tutorial on the image calculator function in ImageJ
Machine Learning in ImageJ/Fiji - StarDist
มุมมอง 10K3 ปีที่แล้ว
Machine Learning in ImageJ/Fiji - StarDist
Adrenaline or Epinephrine; what should we call it?
มุมมอง 1.2K3 ปีที่แล้ว
Adrenaline or Epinephrine; what should we call it?
ImageJ in a Browser - Part2 (3D plugin & Full VR)
มุมมอง 8483 ปีที่แล้ว
ImageJ in a Browser - Part2 (3D plugin & Full VR)
Artificial Intelligence & Image Analysis
มุมมอง 6K3 ปีที่แล้ว
Artificial Intelligence & Image Analysis
Analysing blots and gels with ImageJ/Fiji
มุมมอง 15K3 ปีที่แล้ว
Analysing blots and gels with ImageJ/Fiji
Using Orthogonal Views in ImageJ/Fiji & Imaris
มุมมอง 9K3 ปีที่แล้ว
Using Orthogonal Views in ImageJ/Fiji & Imaris
Background subtraction in imageJ (3 ways)
มุมมอง 71K3 ปีที่แล้ว
Background subtraction in imageJ (3 ways)
thank you so much, its really helpful!!
Thompson John Gonzalez Christopher Thompson Elizabeth
Thank you so much! I have some questions, first, is it possible to train the classifier using more than one image? And second question, is using Stardist for training the model will give better results?
hii. i want to learn how to measure area of tympanic membrane perforations using image j software. please me guide me an approach how can i learn
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Thanks for the perfect summary
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hello. I have a question.would you please help me?I want to count the number of grafts inside the plates with the Fiji (filament detector). how can i do that(can i have your email address i want to send photos of analysis)
hello. I have a question.would you please help me?I want to count the number of grafts inside the plates with the Fiji (filament detector). how can i do that(can i have your email address i want to send photos of analysis)
I have imaged gfp and rfp tagged protein and after merging both the channels, it is giving orange color, instead of expected yellow puncta. What could be the reason?
Hiii, sir craig! whenever I use Fiji to analyze the particles in my image, I set it to exclude images that are on the edges, but it still considers them. Has the same thing happened to you? Could you help me?
Great video ! All of the information are very useful :D
Quite insightful lecture,. Thanks
Very interesting!
Dear Craig, thank you for this informative video. I would like to ask when I try to set a threshold, I see the background as red, not the sample I stained. What could be the reason of this?
Terrific. Now I would like to learn how to quantify size.
Thanks
Hey Craig, I have been using chatgpt to enhance marco functionality instead of writing it from scratch and that is where I think it shines. For example I would record my work flow in Fiji with the macro recorder. Then I would give the code to ChatGPT and tell it I want to do this analysis in all files of a single folder. That works like magic
That’s a great idea. Thanks for sharing. Cheers. C
Great Ex-planation, helped a lot in my thesis!
Very helpful! Thank you :)
A very incredible concept!!
Great video, appreciated the explanations made this a lot easier to understand. Also love the Scottish accent!
Thanks for your video, I have a question How if the color of the cells and the background quite similar? Do you have another method for this case?
Hi, sorry for the slow response. If object and BG are too similar then you may need an object classifier rather than a pixel classifier. Have a look at the Ilastik program. C.
Excellent video! Thank you for making and sharing with us.
Your is THE BEST CHANNEL on TH-cam!!! Thanks a lot for all the videos you are making!!! 🙏
Hi, I followed this to make the macro. But somehow, my macro is usingthe same image again and again. Could you please help? Thanks
Hello! I guess you started recording the macro before adding the image. Then, the first thing that your macro does is to load the same image. I suggest that you open your image before starting the macro, and then you start your processing that you want to do. As a tip, the first thing to do is rename your file in your macro to a temporary name, so all the images that you run with your macro will work with the same script. Once you finish, save the macro and install it as Craig shows, and then you can test your macro. You should be able to open your image first, and then run the macro and should work fine!
Where are you at with this project? I have some fun ideas to give you if you are still working in this field. I write grants if that helps too and know of a way to put this project and the main idea I wanna share into a format for field forensics and ER mop ups etc. If interested in rapping boot it reply and we’ll go from there.
Hi Criag, Thank you for the detailed videos, they are very helpful. I am a novice imageJ user and am trying to characterize spheroids (3D cellular circular structures) that are touching. The watershed function did not work the same way it did in this video. What would you recommend as a next step to try. Many Thanks, Brooke
I was missing the "set scale" part before setting scale bar, found it then on another tutorial
Hello! Thank you very much for this very clear tutorial! I used to do the thresholding manually in ImageJ, but now I want to automate it by linking Ilastik and ImageJ. Do you think it's possible to do it within a macro? if you could help me please ?
Hi, i am New in imagej and Hacer a question if could you answer please? İ am trying on one image that selecting multiple rois and want to for each roi apply crop, duplicate , add gray,Binary.......and skeletonise. Making it step bu step so bored. İ tried to make a macro but i failured. Can you help me please how can i handle. Thanks
This. Is. Awesome.
Hi Craig, thanks for the wonderful videos. Could you make a video on how to use ImageJ to analyse gray cast iron microstructure? For instance, the estimation of graphite flake length, volume fraction and size. If you need some images for the analysis, kindly let me know.
single-handedly saving me in the late stages in my master's once again. thank you sincerely so much for this content. <3