MicrobeHunter.com Microscopy Forum

Hi folks,
What software do you use to measure the subjects on your images?
I've been using Piximetre
http://www.piximetre.fr/
Just looking for other options.
Thanks

I would highly recommend ImageJ. ImageJ is a completely free image editing and manipulation program made with US government funding. It is used in countless scientific publications and has great modules etc that people have written for it. The whole purpose is to analyze images for scientific investigation. It is written in Java and works on any operating system. Heck, may even be on phones now I have no idea.

https://imagej.nih.gov/ij/

mnmyco

ImageJ by itself opens up a potential nightmare of dependency
problems. The collection of modules that make up imageJ are
being added to and modified on a daily basis and not always by
Java experts. What works today may not work tomorrow. Problems
may range from subtle to system crashing events.

Fiji ( Fiji Is Just ImageJ ) solves all the problems. It's free
and updates itself.

see:

https://imagej.net/Using_Fiji

Have fun.

Brad

Good info, Brad_.

And here's a quick tutorial on putting a scale bar into an image:

https://www.swarthmore.edu/NatSci/nkaplin1/scalebar.htm

@Brad:
I have used ImageJ (not FiJi) a lot in the past, including programming of Macros, and did not encounter any particular problems, other than some inconvenience because of the logic of the macro commands. I ran it on a Windows 7, I7 CPU-64bit-6GB memory PC. Perhaps it depends on certain ImageJ plug-ins one adopts.

@wporter:
Thanks for the link.

I like the freeware software "MICAM". It is a lightweight, so very small, easy but very functional.
Info and download http://science4all.nl/?Microscopy_and_Photography

Hobbyst46 wrote:@Brad:
I have used ImageJ (not FiJi) a lot in the past, including programming of Macros, and did not encounter any particular problems, other than some inconvenience because of the logic of the macro commands. I ran it on a Windows 7, I7 CPU-64bit-6GB memory PC. Perhaps it depends on certain ImageJ plug-ins one adopts.

@wporter:
Thanks for the link.

Me either. I have ran ImageJ on linux, FreeBSD, MacOS, Windows 98, 7, and windows 8 and never encountered a single crash unless I was trying to install modules that were not in the download from their website. The only issues I have ever had were from open source java implements on linux.

mnmyco

Thanks folks,
I've played with ImageJ / Fiji in the past but not for this use.
Guess it's time to give it another try.
Thanks ImperatorRex, I had a quick look but that is image acquisition as well as measuring, I'm only after measuring software.

!!! this post deleted

I have ALWAYS wanted to use Piximetre, but alas, I am on MacOS, so, I used Fiji, I came across a plugin that does measurements and added it to my set up. This is huge for Mycology microscopy as for measuring spores. Here is my forked version of the plugin:

https://github.com/Elaniobro/Microscope ... ment-Tools

Being the fossil that I am, I use hardware to measure.

I'm not positive that everything I do is exactly accurate. However, I recommend getting a stage micrometer. Take photos of the micrometer using each of your objectives. Superimpose the photos on what you see in the microscope to measure the size. The photos can be used to make size scales in your images. I even made rulers on cards that enable me to estimate sizes from the video screen (I only view through my camera onto the computer screen).

Just to mention that you can find basic measuring and scale bar creation in Photoshop (at least Photoshop22 for Mac). The last item on the Image pull-down is Analysis. There you can enter and store distance-to-pixel calibrations from photos of a stage micrometer as others have described, use the calibrations to do direct measurements on images, and create scale bars.

Of course, Photoshop doesn't have some of the nice features that a dedicated microscopy measurement program would have. However, it provides good flexibility for making scale bars (scale, size, positioning, font, color, etc.), and the Ruler tool is easy to use with the stored calibrations. Some familiarity with Photoshop is necessary (layers and tool presets, in particular).

For MacOS users, piximetre is a no go. I have been using Fiji (imageJ) with great success. I also found a measuring plugin that "worked" but had some bugs. I forked it and fixed it and wrote a comprehensive Read me.

https://github.com/Elaniobro/Microscope ... /README.md

To provide more detail on using Photoshop to make scale bars:

1) photograph a stage micrometer with each of your objectives;
2) import the images into PS;
3) under the Images tab in the top navigation bar, scroll down to Analysis;
4) you can use the Ruler tool to create a calibration for each objective, i.e. 100µm on the micrometer = x pixels;
5) store the calibrations as Presets.
You only have to do this process once, unless you change your setup.

Whenever you want to add a scale bar to an image, just:
1) go back to Analysis,
2) use Set Measurement Scale to choose the calibration preset for the objective you used,
3) still in Analysis, select Place Scale Marker. That takes you to a dialog that lets you choose things like the length of the bar, the font size, the location of the bar, etc.
The Place Scale Marker command also creates separate layers for the text and the graphic (bar) that you can use for modifications later.

The first time may take some fiddling and exploration, but once you get the hang of it, placing scale bars just takes a minute or two (assuming you remember to do it ...).

Cheers, David

ddy5 wrote: ↑

Wed Mar 22, 2023 2:54 pm

To provide more detail on using Photoshop to make scale bars:

Great description. Thanks.

mnmyco wrote: ↑

Thu Oct 18, 2018 1:32 pm

I would highly recommend ImageJ. ImageJ is a completely free image editing and manipulation program made with US government funding. It is used in countless scientific publications and has great modules etc that people have written for it. The whole purpose is to analyze images for scientific investigation. I agree that she is the best of all. Competitors tried to create something, but everything else ranks lower. I've been tinkering with the world of programming for a long time. I recently read about how we build custom applicant tracking system recruiting needs, and found a blog article for this. This is actually very useful knowledge and worth developing. There is also Fiji, but as I said, this is a secondary program. It is written in Java and works on any operating system. Heck, may even be on phones now I have no idea.

https://imagej.nih.gov/ij/

mnmyco

Personally, I am too recommend ImageJ, it is free and has a wide range of features for image analysis and measurements.