A beginners guide to ImageJ (and Fiji) 

Thank you. This is much appreciated.

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

Great, I appreciate the comment. Thanks. C

Thanks. Good luck on your imaging journey.

Thank you. 🎸

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.

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.

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

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.

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.

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?

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

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.

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.

@@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

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

@@CraigDaly thank you very much

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.

@@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?

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

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.

@@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 🙂

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

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

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.

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

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

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.

@@CraigDaly sur sir thank you.

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