A beginners guide to ImageJ (and Fiji)

[@fauziaquadir7769]

Best beginners video that takes you through ImageJ

[@aysemusaogullari7216]

This is the best ImageJ tutorial video ever! Thank you so much for putting this together.

[@declanmoran1571]

Just started a project using Fiji. Completely new to me and this was really helpful. Thank you so much!

[@vimalsingh6917]

You are an excellent teacher and I have learned so much as a starting point in my masters thesis project.

[@CraigDaly]

Thank you. This is much appreciated.

[@susheelkumarjoseph1299]

Today is the first time ever I thought of using Image J for my histological analysis, and I found this video, hurrah! This is all I wanted as a beginner to start with Image J. Thank you, Sir! The video Is very useful, I would happily recommend anyone who wishes to use Image J or Fiji.

[@CG-ud6my]

I am tasked with using ImageJ to sharpen my SEM images for a research paper- thank you for the intro

[@phillipang5189]

Thank you so much for this! ImageJ has always been a daunting thing for me to learn. This is the best series that I've seen!

[@CraigDaly]

Thanks Phillip, I appreciate you taking the time to comment. Craig.

[@MJs-85]

Incredibly useful! Gona watch all the vids in this series. Thank you, Dr. Daly

[@thibodoux]

Thank you so much! This has been extremely helpful! I've been exploring this program for several days and this answered so many questions!

[@fl4624]

Thank you so much for the whole image analysis playlist, and especially this video! It was a great starting point for my master thesis, and really helpful.

[@CraigDaly]

Great, I appreciate the comment. Thanks. C

[@md.mizanurrahman5825]

Thanks a lot. So useful introduction ever I have seen on Image J.

[@Tspbml]

Waoh This tutorial is such a gem! Saved me from my dissertation! Thank you for uploading this

[@silviacubela621]

The best ever class of FIJI

[@rathaiahyv3469]

nice presentation. looking forward for more videos

[@mariammorgham4864]

thank u for all videoed

[@BrookeCampbell-ub1ek]

Excellent video! Thank you for making and sharing with us.

[@2007redjoey]

thank you for sharing this video. I have just started learning image processing and how to do it with ImageJ. This introduction was really helpful.

[@CraigDaly]

Thanks. Good luck on your imaging journey.

[@AnajuNaranju]

Thank you for this video, it was very useful. I am just starting with Fiji and this helped a lot.

[@jonhawkins1990]

This is bloody good. In industry and using grayscale to assess optical power densities for a medical application. The video has taken from 0 to 90 in 40mins. Worth every second except the guitar playing, which was good, but it's 10 seconds during which another pearl could have been delivered.

[@kp4508]

Your intro rocks ☺️ Thanks for the tutorial!

[@CraigDaly]

Thank you. 🎸

[@abolfazl.dehkohneh]

I can't thank you enough! that was wonderful!

[@carbonara_jina]

These are really helpful! Thank you so much for this online tutorial :)

[@mohamedelgamal6333]

Many thanks for that great video...a follower from the engineering background

[@adamcordes]

Thank you so much for a great video. I learned a lot from it! I have one question. I am doing measurements of cell walls on SEM images. After measuring from a straight line, I fill it, to save the measurement on the image. How can I change the filling color so all the different fills will always be yellow for example?

[@ObasaVictoria]

Quite insightful lecture,. Thanks

[@MrsSunnyfrog]

I agree with the others! Thank you so much!!

[@pablufu]

Thank you for your science public service! Really amazing. Any chance you have one on creating ratio images (division of two colors)? I am struggling as my images need thresholding. The result division image usually just looks like one of the channels, not an actual division, and all objects now have the same brightness...

[@CraigDaly]

Hello, I haven’t made a video specifically on arithmetic functions although I think I do touch on that in the background subtraction video where we subtract one image from another. I will have a look at division now you have requested it. Next up is contrast enhancement that was asked for a few weeks ago. I’ll put your request on my list of ‘to do’ videos. Thanks for watching.

[@dolcevita6715]

thank you so much for this! really helpful ! best lessons ever!

[@HiraJaved-kl6fy]

hi! your content is amazing and I have a request can you also explain how to guess which function should be used on the images while observing them.

[@CraigDaly]

Hi, It's a good question but really difficult to answer. I think the main problem is that you need to know what is available in terms of routines and plugins. You also need to have been using ImageJ/Fiji for quite a while in order to have an initial idea of how to tackle an imaging problem. Having said that, in the large majority of cases we are either measuring, shape, number, size or overlap (colocalisation). Prior to that we probably need to pre-process, maybe contrast, deconvolution, smoothing etc. Every problem will need a different solution but its normally composed of similar aspects to those listed above. that's really just a long way of saying 'it depends' and 'you need experience'. Assuming I have interpreted your question correctly. Best wishes and good luck. Craig.

[@pantuabafras9899]

that was very informative. Thank you very much.

[@Arshaqueh]

hii. i want to learn how to measure area of tympanic membrane perforations using image j software. please me guide me an approach how can i learn

[@hayleywaller2099]

Thank you that was really helpful!

[@adetonaademola4117]

This is brilliant. Thank you

[@susheelkumarjoseph1299]

Also, Prof. can you please let us know where we can learn advanced ImageJ, I mean, further lectures including 3D, etc.

[@priyalvisavadiya3552]

thank you so much for this amazing video, it has been really helpful to me

[@EileenRedmond-f5i]

Very helpful! Thank you :)

[@CC-dh1pi]

Hello Craig, I am a final year medical Physiology student and currently doing my final year project and ImageJ is the software that I am using. I'm having some difficulties regarding measuring nuclei, and in need of some help. I was made aware that I have to add in a NII plug in which i'm not too sure how to do as this is all very new to me. I'm only 5 minutes into your video and hoping that by the end I would have more insight. BTW Thank you in advance for making this video

[@CraigDaly]

Hi Cara, I have not heard of the NII plugin. Could it be Nifti? Which is a file format. Have a look at my video of measuring shapes as that uses nuclei images (I think - cant remember). Is it just a shape and size measurement you need?

[@monakhalid3677]

thank you so much, its really helpful!!

[@highway2chill]

Can you make a video on how to normalise fluorescence intensity between images of different conditions of the same experiments. Thank you so much for all the help you provide 😊

[@CraigDaly]

Hi Tamal, that’s a good idea. I’ll do that one soon. Have you looked at the ‘Enhance Contrast’ option? It has a normalise function that will adjust all pixels values such the the full range is used (ie 0-255 for an 8 bit image. There are another couple of options. It would make a good short tutorial. Thanks for the idea. C.

[@CraigDaly]

Hi Tamal, it took me few weeks but I followed through on your request. Maybe not exactly as you asked for but hopefully gives you what you need for your experiment. Craig.

[@highway2chill]

Thanks for the video. Now i know why i should not tweak a image before intensity measurements.

[@ElectronBombardment]

I was missing the "set scale" part before setting scale bar, found it then on another tutorial

[@nischalsharma1032]

Your beginners guide is really helpful. Thanks for such an awesome lesson. However I have got one query. I am using Fiji software and may I know why do I see an exponential rise and then fall in my graph for an average intensity obtained from z-projection in the concatenated stacks while doing a plot profiling even when the line is drawn in the regions where there are no fluorescent features? Like for instance, control where there are no cells/features.

[@CraigDaly]

That’s a strange one. If you run the mouse over the dark part of the image does it display higher values than expected? Is this an 8-bit image or RGB. My first thought would to make sure your z-projection image is 8-bit, one channel. Maybe even save as a .tiff, close and reload it. After that, I think I would need to see the data to make a better diagnosis.

[@eliyahomar]

Thank you so much ....very helpful.....

[@ambadattpant22]

Great…. Helpful for beginners

[@souheilasemache6142]

Thank you so much! Good evening...I have a question...I have a picture of concrete beam with cracks...i want to measure the width and the crack opening is the distances between the cracks. can I use this software is yes how please?

[@CraigDaly]

Hi. Yes ImageJ could work. I assume that your concrete block is grey (or painted) and the cracks are black or darker. First make the image type 8-bit (not essential but might simplify). Apply a grey lookup table. Next invert the image to make the dark cracks bright and the block dark. Use the tools icons to draw a straight line perpendicular to a group of cracks. Select ‘plot profile’. The result should show a series of peaks and each peak represents the intensity of the cracks. From that graph you can measure crack width and distances. If none of that makes sense, watch my tutorial on measuring blots, it uses the same sort of technique. Just imagine the blot is a block with holes in it. That’s the best I can offer without seeing your image. Good luck. Craig.

[@souheilasemache6142]

@@CraigDaly Thank you very much . Can I send you a picture in the e-mail and put a video on it because I do not understand well and I do not know the program well, please help me

[@CraigDaly]

@@souheilasemache6142 hi. Ok, find me at University of Glasgow and email an image. It might take me a day or two to respond. C.

[@souheilasemache6142]

@@CraigDaly thank you very much

[@ann-cathrin860]

Soo helpful, thanks!

[@BrokenSofa]

This. Is. Awesome.

[@sharoncunningham5002]

Hi! Fabulous explanation :-) I have images of cell clusters (GFP-positive hepatocytes in immunostained liver sections) that I am struggling to count accurately using the basic ImageJ functions; different intensities and irregular shapes, and difficult to separate the adjoining cells. I tried the watershed method but the output looked like spiderwebs! Wondering if you had any suggestions. Thank you so much in advance!

[@CraigDaly]

Hi, two things come to mind. Do you also have a nuclear stain? I wondered if you could just measure total fluorescent area, divide by number of nuclei and get a rough idea of cell size and number. Nuclei are relatively easy to segment - check out my Stardist videos. Second idea, try the Weka Trainable segmentation. I just uploaded a video on that this week. It might help get you a result that the watershed can deal with better.

[@sharoncunningham5002]

@@CraigDaly Hi Craig! Sorry for the delayed response. Thank you SO very much for your suggestions, all extremely useful. One of y colleagues has been trying the Weka strategy as per your suggestion. It's an amazing technique. Again, very appreciative of you taking the time to give your assistance 🙂

[@mdaltinisik]

Thank you so much! I have one query. How can we overlap three intertwined imaginary circles on an image and perform thresholding analysis independently on the innermost circle and the outer rings?

[@CraigDaly]

Sounds like a good short answer exam question. Seriously, can I use it? 😀 My guess would be along the lines of creating circular regions using the ROI manager. However, I don’t think ImageJ let’s you threshold on the region only. So, my long way round would probably involve photoshop to crop the circular regions and then take those back to ImageJ for analysis. Sorry, that’s the best I can come up with at the moment. C.

[@mdaltinisik]

@@CraigDaly Of course you can :):) Thank you so much Dr Daly, I'm following you.. Do you have a social media account in Twitter or Instagram?

[@CraigDaly]

@@mdaltinisik hi. Thanks. I’m on Twitter. I don’t use Instagram much but really should. I’m @CraigJDaly on Twitter.

[@calmdown1992]

Great video!!

[@shaguftabatliwala5261]

It is so useful, thanks!

[@shaileshvarade]

How to measure the velocity of a rising bubble in any solution using Image J?

[@CraigDaly]

Hi, first thing I would try is the particle tracking plugin. Might have to use Fiji to get the plugin. Can’t remember if it’s in ImageJ as standard. C

[@jaiyeolatunji3324]

You are an excellent teacher and I have learned so much from this clip but i have a question. From my curiosity, do you think this application can be used in civil engineerig field of study, maybe for sensors or structural integrity?

[@jaiyeolatunji3324]

oh, and in addition, I am actually a civil engineering MSc student

[@hamtaro3333]

Thank you so much 🥺🥺

[@cookiesgmt]

Very useful

[@PriyanshiChaturvedi-ns1wn]

Can ImageJ or Fiji use pictures clicked from an android phone?

[@CraigDaly]

Yes, both can open a wide variety of file types.

[@劉新浩-f8w]

What is FAD mean?

[@CraigDaly]

Hi, I can’t remember the exact content of this video. Can you remind what the context is? Thanks.

[@sandhyaprakashyj9488]

Hi sir I'm an postgraduate agricultural student in statistics from India in currently going to do an image analysis using maize(cob) image to predict yield actually I referred an article released by CIMMYT they have used this software to analyse bt they had cob analyser option in plugins folder bt while I open it is not there can u plz help me it'll be very helpful for my thesis plzzz

[@CraigDaly]

Hi, I looked at the paper you refer to. They are using Fiji. Are you using ImageJ? If so, install Fiji and try that. Craig.

[@sandhyaprakashyj9488]

Ok I'll install that & try so thanks for ur reply sir

[@sandhyaprakashyj9488]

Hi sir it's me again I have been trying to find that plugin in Fiji too bt it's not there and i don't know how to include can you please help me out sir

[@CraigDaly]

Hi, I looked again at the paper. It looks like they are using a plug-in called ‘ear analyser’. I can’t find it anywhere. I think your best move is to email the authors and ask them to send you a copy of the plug-in. Craig.

[@sandhyaprakashyj9488]

@@CraigDaly sur sir thank you.

[@daline2318]

Thank you!

[@sencerkaya1]

Thank u

[@umutcankzl7814]

Eywallah ustad

[@tejasshirore825]

helpful!

[@jbnOracle]

Next Guitar class

[@supriyashakya5488]

🙏

[@DeloresCastillo-k1d]

Walker Donna Wilson Brenda Thompson Carol

[@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 of analysis)