Tutorial 01 Installing and Basics of ImageJ 

Much appreciated. I'm also new to image processing and I'm a bit overwhelmed. Thanks for the overview and the good description of grey scale.

Thank you so much! I wasn't aware of the montage capability. I had been stitching together images using photoshop. Talk about tedious! More tutorials, please!

Hi! Thank you a lot for this video. I'm a mining engineer and I have plans to work with Image analysis in my PhD.

Thank you for this tutorial.. I am a beginner with ImageJ, this is helping me a lot..

Awesome video, but I had a question. How would I go about analyzing the "brightness" values that you described along a specific line? I was hoping to be able to designate a given line on an image and then be able to generate a chart which would have the brightness on the y axis so that I could see trends along specific lines... Is there a way of doing this all from within ImageJ?

thank you so much, very helpful! I wish you had more tutorials!

Thank you for the response. I figured it out though by installing the "drag & drop installation" function, then installing your plug-in by simply using this feature. Maybe useful for others who have problems with installation on their Mac.

Hi, I have an image (SEM-micrograph) with a scale bar below but I need to know the magnification. Can I use ImageJ to find the magnification?

Thank you for the video. I need to perform cephalometric analysis on a bunch of facial x-rays for which I have to mark two independent lines and check the angle between them.Can you help me in this regard? Thanks in advance!

Excellent! I'm hoping to use imageJ to simulate a virtual learning environment for plant science students. hopefully this will work, I may have questions in due course!

Comprehensive explanation. Extremely helpful. Could you please upload more tutorials?

Hi. The easiest way to get imageJ on the mac would be to download ImageJ from the main site and then also download the plugins only bundle from the MBF imageJ website (MBF ImageJ > Installations) from the menu. You then find your imageJ folder on your hard drive and replace all of these folders with the macro and plugin folders you just downloaded from MBF. Another option is to download Fiji ImageJ which is already full of useful plugins and downloads as a single package on a Mac. Good luck.

Thank you very much! You really helped me :)

Very helpful, Thanks.

Excellent teaching style.

really usefull for me! thanks a loT!!! love it!

Hello, am wondering why you have set the scale according to the Olympus magnification 20x ? and what will happen if we do not set the scale? thanks

The MBF website is down, MBF plugins can be downloaded on the ImageJ website : imagej.nih.gov/ij/plugins/mbf/index.html

Can we use Fiji to alter the brightness of multiple images at once? Like, "apply to all" kinda option Reply

The Merge/split shortcut can be reached just by going to 'Image'-->'Color' . The menu you reach there has all of the same functions. The only thing missing is the pretty pie graph :(

Where may I find the tools you were using, for example, the merge/split color tool or the histogram tools?

very nice detail tutorial. do you have a tutorial about how to write imageJ plugin?

Hey! Is it possible to detect colored particles and fibers with this program? I mean not just counting the pixels which are colored but to count particles. Thanks in advance :-)

Very good introduction. At 4:55, it is a Java application, not JavaScript. They are different.

Hello, I watched your video because I'm planning to use ImageJ as a tool for the analysis of data and results of my master's thesis. I would just like to ask some simple questions that I have about using ImageJ: 1) Is there a functionality or option in ImageJ that allows the user to count the number of pixels of a particular color and/or get its percentage from the total number of pixels? For example, I have an image with color A and B, I want to get the percentage of the total number of pixels of color A, or color B. (For simplicity, we can let color A = black, and color B = white) 2) For getting the percentage of total number of pixels, which ImageJ would you recommend for me to download and use, the basic ImageJ that you first showed in the video or the MBF ImageJ which you used in the video? I would really appreciate if you could respond to my queries, it will be a great help. Thanks in advance.

Thank You :)

Hello I downloaded (fiji is just) ImageJ, i am trying to cut parts from my 3d viewer but as soon as I select "freehand selection" (or any else selection type) my fiji software crashes and quits on its own (btw i have installed it on my Ubuntu 16.04). Can you please advice me what should i do to resolve this problem. Thanks in advance :)

Nice sir

Thank you so much

Hi I hope you can help me. I am analysing Retinal Fundus Photographs which I have taken in high resolution images. I am using NeuronJ plugin to trace the retinal vessels and get a binary image of those traces. However, in NeuronJ it does not allow me to open the images unless it is an 8-Bit image. But when i convert my images into 8-Bit image, it loses a lot of the detail. How could I open my image without it being converted into an 8Bit image where it loses a lot of detail. I hope you can help. Thank you

Hello, thanks for the video. I was trying to download the MBF ImageJ for 64 bit -widows 10 via the site that you mention, but it seems that I have to create an account to oracle in order to do so. Is it any other way?

Thank you

Are you using a plugin for tweaking the RGB channels and histograms? I can't seem to find the exact one you are using.

There is no way to download the RGB montage plugin...can someone help me with this?

Hi, ImageJ is a java programme, so doesn't actually have to be installed on a computer, it could even run off a USB stick. It sounds to me as if the programme didn't install properly on your computer. Try uninstalling it and then download either the MBF imageJ bundle or even the Fiji ImageJ bundle. Once installed you should be able to increase the amount of memory ImageJ can use by going to through Edit >Options >Memory and Threads and then increase the memory to whatever you can. Good luck

Fiji also can be used, which is based on ImageJ and include a lot of plugins in an ordered way. fiji.sc/Fiji

I need to count overlapping circles using image J. Could you elaborate the procedure?

I can only run your folder if I go directly to the plugins folder and double click on the ij.jar icon. Then it opens Image J, but it only has 128MB of working memory and cannot be adjusted. This is not enough to do anything meaningful with an image besides open 1 file to look at. Is this how it's supposed to run?

HOW WE CAN CALCULATE PERCENTAGE OF CELL POSITIVE FOR EGFR IN IMMUNOHISTOCHEMTRY STAINED IMAGE . I ALSO NEED TO CALCULATE TOTAL NUMBER OF CELL PRESENT IN THE IMAGE? CAN SOMEONE HELP?

Sorry I coundn't find the RGB splitting button or plugin. Can you please send me a link to install it? Bests

When will 02 be out?

Where can I find the MBF imageJ? The site that you mentioned seems to be dead

is the procedure still the same for downloading it?

Hi I am looking for an analyst who could uese D-strech

I'm not clear on the installation process for Mac OSX.

Unable to download that version anymore.

Thank You for your tutorial. The download of ImageJ microscopy is not available in the site. It will very helpful if you will provide me link to download this file. Thank You. Waiting eagerly for your kind reply.

Good video, I have one question, I have problems with open a image in format TIFF, the software say me that ImageJ can only open 8 and 16 bits/channel images (12), my pictures are 24 bits but I read the manual I undestand that ImageJ can open to 32 bits pictures, Can somebody help me please? Excuse me for bad english

Try Fiji.... it's a much better way to do ImageJ

very confused

get a popfilter please. my poor ears

please stop raising the tone of your voice at the end of every sentence making every sentence sound like a question.