Intro to ImageJ/Fiji

A brief introduction to simple image analysis functions in ImageJ/Fiji. This is a recording of a Zoom meeting led by HCBI Director of Imaging Doug Richardson.

[@boobycrafty3707]

this is so helpful. I'm an undergraduate sophomore at UPenn who is working on a bioimage analysis project with Ilastik and has experienced so many roadblocks over the past few months. Thank you so much for putting this out!

[@terrylaitw840]

Very informative, glad I haven't started counting all the cells with naked eye and a counter in my hand...

[@user-cx3cz4mv5b]

Super helpful. highly appreciate it.

[@shaileshvarade]

Hey, thanks for your video. It was wonderful to learn so much about ImageJ. I just had a query, how to measure the velocity of a rising bubble in any solution using Image J?

[@swimfast8076]

Hi. I am wondering if I could use this software to analyze normal pictures? They will come from a normal camera (JPG, Panasonic Lumix DC-FZ80)

[@PoetrybyManas]

Thanks for that! COuld you please tell me how do I use the erase tool? Right now it is just blackening the area when I am using the erase tool. Not sure why is it so. thanks.

[@silviacubela621]

Thank you very much, could you please add me to the participant list? I work at the Diabetes Research Institute, Univ of Miami, and basically, my work is using confocal microscopic.

[@terrestrialxploration3560]

I enjoyed this and it was helpful learning about the processing pipeline, one thing I didn't see is how to calibrate and I believe this is important and I have not learned how to properly calibrate, do you have any idea how I could learn how to properly calibrate my images?

[@AveenJalal]

Hi, Thanks for the explanation. what are these different series that open when I am trying to open one image? and how to choose the right series? originally, I was thinking that these series are the images of different samples I have taken on the microscope. if this is the case, then how can I know which image is which? because I have named every image differently for example control, treatment 1, treatment 2. and the series do not mention that.

[@pranavrana2589]

How do we use it for calculating porosity

[@aa-so4nj]

Thank you for the detailed explanation

[@KuroNoDarkside]

Thank you!

[@muneebhussain1373]

legend! thank you

[@saliyasb6167]

Hello I have a query, how to calculate probably paramter for irregularities (PPi)

[@christopholies5617]

Hi. Do you know if there is a way to manually cancel detected 'Blobs' during tracking analysis? or to manually scrub noisy areas so that they are not misidentified during binarization? Thanks

[@doughnut469]

I have an area and want to measure its value. So i put a polygonal figure to the place i want to measure it. I go to analyze than measure. Now instead of a picture, i want to analyze a video with 100 pictures. The place I measure stays the same. How do I do that without pressing measure after every picture?

[@johanna.m.dela-cruz]

Have you tried thresholding? For a video, you can convert it into a virtual stack , then you can do analysis on an ROI on the whole stack.

[@neginj1981]

Oh hi son!🥰

[@xeramainali9270]

i cannot open sample image in FIJI. it shows blank

[@jacquelinelabovitz4613]

you are amazing, thank you!

[@Archimede5917]

I took pic with my camera and I have some refexion on one part of the zon I want to mesure. Because of the flash I can not anything. Is it possible to suppress it ?

[@XxXnonameAsDXxX]

I am afraid not, you either have to cut out your artifact (flash) or retake your picture.

[@Archimede5917]

@@XxXnonameAsDXxX Okey thank you for the answer !!

[@XxXnonameAsDXxX]

@@Archimede5917 No problem. Artifacts are very usual even with relatively good microscopes, you can have dust, uneven lightning etc that can cause you extra problems. You will get used to it

[@christopholies5617]

When you say 'memory' at the start you mean RAM (random access memory) right?

[@harvardcenterforbiological8767]

Yes, that's correct.

[@christopholies5617]

@@harvardcenterforbiological8767 thanks for replying even though it was a silly question. just wanted to make sure. I've been trying to use ImageJ to track insect locomotion but it keeps crashing when I try to import an mp4, do you know if there is a pluggin that I need to enable to allow it to function?

[@TuanLe-ms4cp]

Can you tell me how to do ground truth annotation with black background and a white dot to represent object (mask)

[@joshuakuruvilla4809]

17:45