FIJI (ImageJ): Ridge Detection [Measuring Line Width & Length]

[@blazehudson2147]

Thank you. Good job.

[@melaniabica-popi4279]

Your channel is so inspiring and educational! Thank you for making such a great job! I would like to ask if I have this type of filaments inside the cells, is it possible to define specific cells with the filaments detected inside and then to measure the particularities of the filaments in each cell? Thank you again!

[@johanna.m.dela-cruz]

Hi Melania (@melaniabica-popi4279). Thank you for supporting my channel. With the right parameters and as long as the filaments are clear enough, I would think Ridge Detection will be able to measure these. You might have to do some pre-processing to get them to be more visible.

[@antolincanto]

I wanted to express my heartfelt thanks for your incredible KZbin channel. Your content has been truly informative and valuable to me. I have a question regarding dynamic area measurement in a photo using a polygon. Do you happen to know if there is any tool that allows for this task? It's very important that it has to be dynamic (live) and allow me a definitive measurement later. Thank you. Great Job.

[@johanna.m.dela-cruz]

Thank you so much for your support. Have you tried if the object you want to measure can be segmented using traditional global thresholding? Once segmented, you can use Analyze Particles to measure area for each image in a time series.

[@antolincanto]

@@johanna.m.dela-cruz What I have to do is select several images always in the same amount of area more or less. My images are retina, so the shapes are complex. What I need is a live area measurement in which I can see if I should take more area or less before taking the definitive mesument. I am trying to do it by coding in java somthing similar to Dynamic plot profiler but till now my results are not very good.

[@johanna.m.dela-cruz]

@@antolincanto you may want to try 1-click ROI tools (custom ROI). I am not aware of a dynamic area tool.

[@PatriciaNerydesiqueira]

Hello! Your videos have contributed a lot to my analysis. This tool is sensational, very practical compared to others. One question, I use the ImageJ 2.14 64-bit version, and it takes a long time for the preview to appear. This step by step video is quite quick. Do you have any suggestions as to what could be causing this delay? Generating results from just one image takes even longer. thanks

[@johanna.m.dela-cruz]

Hello Patricia. How big are your images. Are they in 16-bit format? Usually larger images tend to run slower. My videos also go a bit faster since I speed up the analysis time intentionally.

[@PatriciaNerydesiqueira]

@@johanna.m.dela-cruz Hi, Johanna, thanks for getting back to me :D. no, the images are in 8 bits. The program actually runs very very slowly, even in preview, and often crashes. and it is updated. I think I will reinstall it.

[@johanna.m.dela-cruz]

@@PatriciaNerydesiqueira you might have to modify your parameters because the algorithm may not be detecting your objects.

[@PatriciaNerydesiqueira]

@@johanna.m.dela-cruz hey! unfortunately that's not it. I came to the conclusion that I have to exclude the branched flakes to leave only the filamentous ones. When I run images with just the filaments, it takes just 2 seconds to simulate. but when with images full of flakes, it takes about 15 minutes and it still considers certain spaces between the branches, or it just stays on "wait" without going back to "preview". Then I have to close, restart and nothing works, I have to force the program to close. And I still uncheck "estimate width, show junction and IDs" I thought that adjusting the width and length range would work, but for images with a lot of flakes it doesn't work well. The images are in grayscale, 8bit, all the plugins I've seen so far exclude unwanted bodies in colored images. Do you know of any tool available that could delete unwanted bodies automatically? There are a lot of images to make manually. and thanks for your help so far!

[@johanna.m.dela-cruz]

@@PatriciaNerydesiqueira you could try filtering.

[@jamilaiqbal202]

Can we use this tool to segment neurites?

[@johanna.m.dela-cruz]

Hi Jamila. I would think neurite images are better acquired as 3D images. Semi-automatic tracing of these neurites via Big Trace might be a better way to segment them. kzbin.info/www/bejne/jJrUl2eqrah2gJIsi=-FArfAeZIfOoSnqS

[@zahraahmadi2234]

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)

[@johanna.m.dela-cruz]

Hi Zahra. If you go to my channel description, my email address should be there.

[@zahraahmadi2234]

@@johanna.m.dela-cruz I can’t find there😅

[@johanna.m.dela-cruz]

@@zahraahmadi2234 If you are subscribed to my channel, under my name, you will find the statement "Listen, watch and learn..." click on more and you can view my email address. Sorry, I can't just advertise openly my email address. You would have to be on a laptop/computer (not phone) to see it.

[@zahraahmadi2234]

@@johanna.m.dela-cruz I use phone and subscribe your awesome channel ( I don’t access a laptop or computer- would you please share your email address here)

[@zahraahmadi2234]

@@johanna.m.dela-cruz I use phone and subscribe your awesome channel ( I don’t access a laptop or computer- would you please share your email address here)