Hi, I have a question about setting threshold. Whenever I change the threshold, it shows different volume results. The measured volume varies depending on the user-defined threshold. How can I ensure consistent and accurate measurements? Is there a way for the program to automatically determine the most appropriate threshold? Alternatively, is it possible to measure volume directly in the 3D viewer without setting a threshold? Thanks aways!

how do you know which cell is # 1,2,3, etc?

I stepped upon your nice channel and discovered by chance that you present the tool that I wrote (KymographClear). Just a major thank you for this and big kudos to your very useful channel :)

What file type would be best to import onto fiji? I have an image stack (.tif) that I want to use with the software. Thank you for the video, it was a great help!

Thanks for the video! I am using this to measure nuclear volume. I was wondering if there is a way to measure the nuclear thickness or height from a Z-stack? Thanks again!

Thank you for this very helpful video!!!!!

This has been a really helpful tutorial. I am trying to quantify LC3 puncta in cells after serum starvation in WT cell lines and some knockouts. How to rule out the false positive in the control cells which gives are mostly without an puncta?

Thank you for the excellent video. I'm having a hard time finding an easy-to-follow tutorial video. Thanks to your video I can run my quantification for my final project

Hi Johanna, Thank you so much for your work in reviewing the plugin and explaining its various features. I really appreciate your effort. I will add the link to your video in the plugin's GitHub repository so more people can access this valuable resource. Thanks again! 🙂

thank you for this.

your tutorial was perfect.thanks a lot

Hi Johanna, I hope you are well :) Do you know of any alternative to using Threshold in macro, so that it automatically matches the result of each image? Because each image generates different values, and there is no way I can provide a fixed value that works for the entire set of images (there are many)

You should publish this in Jove so I can cite you!

This video is EXTREMELY helpful and informative. It is a challenge to navigate through all of the myriad algorithms available within FIJI, specifically regarding registration. Thank you.

hello，After stitching the pictures, there is a black line between each pair of pictures. How can I remove this boundary line?

Great video I followed all the step but for some reason it’s not loading when I press measure. Can you please help. Thanks

Awesome! Thanks for your hard work!

Thank you for this video. I tried using this video as a guide to automatically measure the volume of breast lymph nodes in a T2 fat saturation MRI scan, which I took my self. I’m encountering problems and challenges with the threshold as it’s also highlighting / segmenting neighbouring structures with similar contrast. Also, I’m unsure of the min and max values in 3D object counter, as the values I’m putting aren’t allowing me to isolate the nodes alone. I’d appreciate your help as this image analysis is part of my masters research project. Thanks

Is there any way to set a ROI so that cells outside of it will not be counted? Additionally is there a way to keep the number labels on the 3D viewer? Or add them after the 3D image is generated? I wanted to look at multiple channels in 3D, but when I add an image, I keep accidentally selecting it and it keeps moving, is there a way to keep it stationary?

How to do caliberation for nuclear morphometry

Thank you, this is helpful!

I have two questions: 1. With the 3D Object counter, I can't get the numbers for the cells to actually show up. There are colored dots on the cells and table says there are cells but they have no numbering on the image. How can I get the numbers (I have already tried changing the size and checking & unchecking the option white numbers)? 2. Is there a way to merge the 3D viewer from from the 3D manager labels cells? I need to be able to see where the cells are related to the other channel of Nissl but when I tried to merge the channels I got an error that the files weren't the same type/size.

Hello Johanna, can i have your email address? I've some questions about stitching images Nice video by the way

Hi am I able to get the macro for this?

if (canSigma) run("Sigma Filter Plus", "radius=" + sRadius + " use=2.0 minimum=0.2 outlier stack"..................why for thresholding in 3D, it does not recognize this command.

Hi, i am trying to do mitoanalysis but i am getting an error, unrecognized command Sigma filter plus in line 194...Could you help me here please?

Hi! Thanks for a great tutorial. When I threshold the image using default settings, I see in the ROI manager that several (individual) mitochondria are getting counted as a single ROI leading to massive numbers in the analysis. Is there any advice on how to reduce this? I used the nyquist equation to set my scanning parameters and I do not see a difference.

Turi ip ip ip... very useful!

My ImageJ crashes when I try to do the thresholding. I can't proceed further 🙁 I have tried uninstalling and re-installing ImageJ. Does anyone know what's the issue?

hi, i want to ask, how to make multiple circle analysis in one image?

good luck

@johanna.m.dela-cruz, could you make a protocol to show a solution about this problem" Fluorescence signals at one emission wavelength were recorded with dual-excitation wavelengths (A and B), the a ratio of fluorescent intensity of A/B was obtained. Next step is to convert the gray scale of the ratio image into pseudocolors. "

Hi there! Is there any way to reverse the segmentation? we have been given 5 images from SEM (ti, si, w, k, and ca), and we are looking to input these different rgb images in one final image. Can this be done on segmentation or will it use different approach? tnx

Thanks a lot !!

Thank you so much for the great videos! I was trying to create a 3D projection of the merge between the object counter and the duplicate of my original image, however I get a message saying that "The source images must have the same depth." May I ask how I can troubleshoot this?

Hi my program freezes when opening the stl file Any suggestions?

Great video. It was very helpful for understanding the MorphoLibJ toolset and workflow. Are you aware of any way to provide quantification data?

Thank you for the video! My pixel width/height doesn't fall in the given range. It is way out 352 um :" what should I do for counting then?>

Thank you so much ! You made me understand 6 hours of class in 2 videos !

Many thanks!!!!!💯

very helpful tutorial!

This is awesome. Thank you for this video. Do you know if Diana allows for analysis of time-lapse images?

Dalton Ridge

I have let fluorescent agent (Protoporphyrin IX) diffuse into some gelatin samples with optical properties simulating that of human skin, and with SFDI I'm trying to estimate how deep the fluorescent agent diffuses. How should I model a PSF to de-blurr my images? I know the wavelengths and I assume a attenuation factor. Any ideas?

Hi, Thank you for the videos they are resourceful. I am trying to track cells in 3D to calculate their angular velocity. I would appreciate some help with this.

Great content subscribed. Hallo, can you perhaps make video about how to count inflamation cell ilfitration on histology? Thank you so much, I really need it.

Hello from Argentina! I've been following you for a long time, and your videos are always great! Do you have any on immunohistochemistry analysis? I know you sometimes organize courses, and I’d love to learn more about them. Thanks!

very good

Stop using this disgusting music, you piece of shit. Just talk over it. Your tutorials would be better if you talked.

Thanks for very good tutorial. Can you share the used dataset?