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Hi Does the weka segmentation work on a stack of images like an mri scan ?

thank u for all videoed

Sorry for adding a bit of a critical comment here, but from a professional Image Analyst's point of view there are some things that are not quite correct and should not be left uncorrected for others who watch this. However, there is by far not enough space in a comment section to explain them in full. First: background is not noise which is not auto fluorescence which is not unspecific staining which is not uneven illumination. And there is no such thing as background-noise. The term is a combination of actually two imaging inaccuracies. One can subtract background but not noise! All of the former need substantially different methods to reduce them: - background can be measured and subtracted pretty much as shown in the beginning of the video. - noise can only be reduced by the imaging and camera setup (e.g. line or frame averaging in confocal systems) and filtering changes all intensities which is only an option in processing but not before measurements - auto-fluorescence cannot be subtracted since uneven and also not be estimated from a unlabeled sample. It needs special technical equippment for taht (spectral imaging and linear unmixing) - unspecific signal can be reduced in processing using the rolling ball or sliding paraboloid method but this is not quantitative and should NOT be used before intensity measurements!!!!! The rolling ball size also has to be determined based on object size not just optically estimated! Creating a background and using the image calculator is just what the "Subtract Background" method does anyways and still is not quantitative! Setting an arbitrary background intensity using brightness and contrast on the rolling ball estimated background image to then subtract something (????) 🤯is definitely NOT an option or by any means good scientific practice. I would be careful with showing those subjective methods to students which might use them unquestioned and then either get accused of image manipulation or simply end up with inaccurate or wrong analysis results. Students should undergo a sound education in image analysis by image analysts either by organizations such as GloBIAS (former NEUBIAS). Additional info for educational workshops adhering to high good scientific practice standards: www.biovoxxel.de/workshops/

Yeah this is great. I couldn't for the life of me string together a search phrase that led me to the Image Calculator. Sometimes boolean operations just aren't called boolean, I guess.

Thank you! I am just starting medical research (analyse of image with AI) and it was quite helpful to have an idea on how the computer works with it. Kind regards!

Hi Craig, thank you for the clear tutorial! I'm trying to obtain the height differences between two surfaces by subtracting two images, but I found there's a drift in x,y and z directions. The lateral directions I managed to resolve by translating one of the images, I'm wondering if there's also a way for z-direction shift correction?

This is bloody good. In industry and using grayscale to assess optical power densities for a medical application. The video has taken from 0 to 90 in 40mins. Worth every second except the guitar playing, which was good, but it's 10 seconds during which another pearl could have been delivered.

thanks for the video. My Fiji Imagej is suddenly crushed and the closed .. do you know why, please?

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thank you so much, its really helpful!!

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

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

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?

Excellent video! Thank you for making and sharing with us.

Your is THE BEST CHANNEL on UA-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

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

Nice Tutorial. Thank You.

Craig, tutorial filter remove unblur photos .

Thank you very much, It's a great video!

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