ImageJ help and advice

morpholibj
Tags: #<Tag:0x00007fb87d597c10>

#1

Hi i have just started a new project using ImageJ and i was wondering if there was someone who i could talk to. I have to measure around 20 different variables on a large bank of photos and i was looking for ways to speed up the process. For example in binary is it possible to automatically measure the maximum distance between two points of a circular object? Is it possible to create shortcuts of multiple steps?
Thanks Gavin


#2

Hi Gavin,
Welcome to the forum! I think it would be easier for people to understand/help if you could also upload a sample image and highlight what you would like to measure?
Cheers,
Praveen


#3

Hi i was wondering if it would be possible to measure the maximum distance between two points on the outside of shape (similar to diameter). I understand it can be done by drawing a line manually but i was wondering if it could be done automatically (without human error)?

Thank you Praveen for your response, Gavin


#4

I believe you’re looking for the “Geodesic diameter” which MorphoLibJ can compute for you:


#5

Thank you i will look into that :slight_smile:


#6

Hi,

I have downloaded the plugin. And try to measure the object given above but this error comes up?

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.51s; Java 1.6.0_24 [32-bit]; Windows NT (unknown) 6.2; 29MB of 1217MB (2%)

java.lang.UnsupportedClassVersionError: inra/ijpb/plugins/GeodesicDiameterPlugin : Unsupported major.minor version 52.0

This plugin requires Java 1.8 or later.

I have tried installing the latest Java but the error message remains.

Thanks, Gavin


Analyze skeleton 2D/3D not working in headless mode
#7

@gavinminty,

If you’re using Fiji, then you should use the “Update sites” to install MorpholibJ.
See here:

  1. Select Help > Update… from the Fiji menu to start the updater.
  2. Click on Manage update sites. This brings up a dialog where you can activate additional update sites.
  3. Activate the IJPB-plugins update site and close the dialog. Now you should see an additional jar file for download.
  4. Click Apply changes and restart Fiji.

then
Plugins > MorphoLibJ > Analyze > Geodesic Diameter

That should do the trick, but please post back to let us know how it goes either way,
John


#8

Installing a new Java doesn’t help, because you’re using a version of Fiji that comes bundled with Java 1.6.0, as you can see from the error message:


So in addition to @bogovicj’s advice, you’ll need to make sure your Fiji actually runs on Java 8. The easiest option is just to download a new Fiji version.

For more options, see the section on Upgrading an old installation on the ImageJ wiki.


#9

Thanks got it to work, thanks a million !


#10

image

So i have managed to input geodesic diameter and it looks great!

I am getting odd results with it though. In this example the line tool measures 33 and the geodesic diameter ( the red line i believe) measures 260. Would you be able to explain the units of the geodesic diameter, or how i can convert it into something comparable, or generally explain this difference?

All the best Gavin


#11

What is the calibration (pixel spacing) for that image? Could be that one of those tools is using it and the other isn’t … :confused:


#12

Hey,

Thank you for your help. One measurement was micro meters and the other pixels and the conversion rate works!

We are having trouble getting the measurement of the geodesic diameter from within the macro to process it further. Is there is simple macro function to get it?