Which Version Should I Use

fiji
imagej

#1

Hello all!

I am new to ImageJ, so new in fact that I am seeking help on which version I should even download. My ultimate goal at present is to analyze corrosion of test panels and depending how this goes expanding my labs use of ImageJ to perform other similar measurements.

Looking at the ImageJ.net website I am thinking ImageJ2 or Fiji would be my top two choices but am looking for feedback from others as to which would be a more long-term solution (ImageJ2 being the newer version), easier to work with at this point in time (plugins pre-installed with Fiji), more stable (ImageJ2 seems to be in development?), etc.

A little background on my problem, it will be similar in nature to these threads: Using imageJ to measure areas undergoing corrosion and Corrosion Thickness Measurement but with a few variations.

My images will all be of flat panels of aluminum (AMS4045 7075-T6 to be specific) that have been subjected to accelerated corrosion testing (ASTM B117). The panels had various corrosion inhibiting compound countings applied that were scribed with an ‘X’ to promote corrosion and after testing the coatings were removed as much as possible but in some cases caused staining of the panels. Due to the thickness of the coatings, we are using a modified ASTM D1654 for evaluation purposes in so much that we had to increase the scribe width and use an ‘X’ verse a verticle line. My images will be obtained through the use of a scanner which I could use to help out the analysis process by scanning photos in color, grayscale, or black&white and at resolutions varying from 75 dpi to as much as 4800 dpi and can save as type BMP, JPG, or PNG. (At present I was planning to experiment with these options to find the best combination but help on this would be appreciated too).

Please let me know if any other information is needed and any input would be greatly appreciated.


#2

@NavyJEB

In general, we suggest new users download and use the Fiji distribution of ImageJ. You’ll get everything you need to do the work you seem to need… And when the time comes and you have more specific questions regarding analysis and building workflows - just post here on the forum once again. We are all here to help!

eta

Side note: Never save images to be used for quantitative analysis as JPEGs! Always use TIFF when possible - or the raw, proprietary file format of your particular imaging system. You can read more on why here.


#3

Thank you for the quick response. Download underwary!


#4

Too - I forgot to mention… one of the ‘powers’ of Fiji/ImageJ is the Updater… you can keep all components up-to-date automatically, etc. Read up on that guy too.

eta :slight_smile:


#5

@etarena I got Fiji from imagej.net site and was trying to follow along with the JPEG section of the Principles page (specifically the Boats script showing Glasbey LUTs) and it seems I have none of the sample images, did I do something wrong or are these files online somewhere and it is an issue with my works network security?


#6

To download the sample images go to “File >> Open samples” and please do what should always be done when new to whatever tool, study the User Guide:
https://imagej.nih.gov/ij/docs/guide/index.html

Regards

Herbie


#7

@Herbie, I have done that but I get a pop-up error message which read, depending on the exact sample selected, “Error loading image” (happens for about 90% of them) or “Server returned HPPT response code: 403 for URL: http://mirror.imagej.net/images/file_name” (the other 10%)


#8

No problems with downloading sample images here and I’m sure it’s not a problem with ImageJ or Fiji.

I understand that you like to download sample images, but the URL you gave us before is not suited for this purpose.

Good luck

Herbie

PS:
You may also have a look at:
https://imagej.nih.gov/ij/images/


#9

Looks like it is likely just a network security issue with my workplace then :frowning: it seems if I go to the mirror site directly I can download the files then load them through Fiji I just can’t select them or use the script.


#10

I just can’t select them or use the script.

What exactly do you mean with select and what kind of script command or function in which language do you mean?

Clueless

Herbie


#11

By select I mean File > Open Sample > Boats (356K) gives me the error “Open URL: Error loading image” but I can download it to my computer from the mirror site I mentioned above and File > Open… works to open the image.

By script I mean Plugins > New > Macro then copying the code from here fails at multiple points.

Obviously the run(“Boats (356K)”) doesn’t work so commenting that out and loading the image manually then running through the rest of the script should work however, the “Save As JPEG” command somehow maintains the same quality even though it does save the image as a .jpg on my machine (a pop-up opens for me to select location and name it versus automatically saving it) so when the “Subtract” command executes it is a solid black image and there is no difference in the Original and JPEG as there should be and as shown here.

I was able to manually perform all of the commands by selecting them from the menus and generate the images seen in the second link.


#12

Thanks for the details!

Please try the following ImageJ-macro:

//run("Boats (356K)");
nme = split(getTitle(),".");
nme = nme[0]+".jpg";
run("Duplicate...", "title="+nme);
path=getDirectory("temp")+nme;
saveAs("Jpeg", path);
close();
wait(20);
open(path);
imageCalculator("Difference create", "boats.tif","boats.jpg");
run("Glasbey");
exit();

Paste the above macro code to an empty macro window (Plugins >> New >> Macro) and run it with the “boats.tif”-image open in ImageJ.

This is what I get:

Regards

Herbie


#13

Thanks! That worked perfectly.


#14

Great, thank you for the feedback and have a nice evening!

Herbie