ImageJ for seedlings length measurement less than 0.4 cm


#1

Hi,

I am new to ImageJ software. I want to measure the seedlings length that are less than 0.4 cm. Could anyone suggest me if I could use ImageJ to measure such length accurately?

Thanks


#2

Good day,

in order to help you we need at least one typical (not best) raw image in the original TIF- or PNG-format. No JPG-format though, because JPG introduces artifacts! You may also post images as Zip-archives.

Furthermore, we need to know how you define the desired length with respect to the specimen.

Please be precise in your explanations because computers have difficulties to deal with fuzzy definitions.

Regards

Herbie


#3

Hi Herbie,

Thanks for your reply. Do you mean JPG formats are not good format for ImageJ?


#4

Exactly, JPG-compressed images are unsuited for scientific analyses because JPG-compression is lossy and introduces artifacts that can’t be removed.

Regards

Herbie


#5

Hi Herbie,

I am sorry if I am asking a very basic question.
I had used jpeg format to measure the seedlings length with ImageJ. Since I used jpeg, was the measurement not accurate?


#6

I had used jpeg format to measure the seedlings length with ImageJ. Since I used jpeg, was the measurement not accurate?

I can’t answer your question, because I don’t know how you analyze the images and how accurate your measurement must be. If you are mainly interested in geometric properties, JPG-compression may not dramatically influence measurements but it depends on spatial resolution of the images as well …

Please show images and explain in detail which processing steps lead to the final results.

Reards

Herbie


#7

Hi Herbie,

Here is how I did the measurements with ImageJ;

.

Steps followed;
Ruler scale was set to pixel scale using straight line.
Free hand tool was selected to measure the length.


#8

So, where is your problem (except for the JPG-issue) if you do the measurements in your images by hand?

With the scale of your sample image you get about 90 pixels for 0.4cm which appears sufficient for rather accurate measurements even in JPG-compressed images.

Please tell us where you see any problems doing the desired measurements and why do you use a physical ruler and what do you expect to measure with it?

Clueless

Herbie

PS:

I just realized that the ruler is on the image which is perfectly OK. Mea culpa!


#9

Hi Herbie,

Sorry for the confusion. This image is for the seedlings > 0.4 cm So, I was not worried about the accuracy of the measurements (I thought it would be accurate). Since, you mentioned before .JPG may not be a good format, I just wanted to show you if the measurements were fine. What do you think based on the attached image?
I have other sets of images with <0.4 cm length. I am not very sure if the imageJ could accurately measure such small length. So, I posted this question before.
The ruler was used to set the pixel with 1cm ruler length. Is there any other way to set the known distance scale to pixel scale?


#10

Is there any other way to set the known distance scale to pixel scale?

Please see the PS of my previous post.

I have other sets of images with <0.4 cm length. I am not very sure if the imageJ could accurately measure such small length.

If they have the same resolution and scale then 0.4cm corresponds to about 90pixels which seems reasonable but what is the smallest length you like to determine and with what precision?

Please show a typical image.
(No screen shot, no phone image.)

Regards

Herbie


#11

Hi Herbie,

I have attached the picture herewith. I found slight discrepancies with the manual measurement. Is there any way to increase the accuracy?

Thanks


#12

Good day,

here is what I get from your sample image with four seedlings


Results
and the length values in pixels appear reasonable!

I see little chance for a reliable automatic measurement of the length though.

Regards

Herbie