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.
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?
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?
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
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.
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
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
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.
Hello Craig, thanks for the great video! I am new to the world of image processing. I will be starting a project to identify fungal spore cells from images taken of microscopy slides (fluorescent and/or polarized). The goal is to train a model which can identify spores between different fungal species. In my case, the spores of the two species of interest differ slightly by size and spore wall structure. Essentially, my end goal is to process thousands of images of spores with a working model (1. identify the spores on a slide image, and 2. determine the species based on known parameters unique to each species). My apologies for the long winded inquiry, but any pointers or recommendations you could provide me would be immensely helpful. I am trying to determine different softwares and/or programs where this could be possible.
