How to measure cell length and width

I have an example photos of my lab result as attached.

I want to measure cell length, width and quantity of cells.

Could you please recommend which program I should use for this situation?

Hello Mint and welcome to the forum!
One way to go about analyzing these images is to use CellProfiler, and using “UnmixColors” module and then “IdentifyPrimaryObjects”.
Best!

Thanks for your suggestion!
I’ve tried using CellProfiler but I found error on NamesAndTypes module like this.


Do you know what’s wrong I did?

This error is most likely a bug in cellprofiler caused by python2’s inability to properly deal with unicode. Try to find and remove any non-standard English characters.

Hi @Mint_Diabolus,

Yes. As mentioned in the above thread you could check the path if the input image, in case you have any special characters. This link might be useful,

To compute the length, you could use Measureobjectsize module and the details are available here ,http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.9/modules/measurement.html#measureobjectsizeshape

In case you are still not able to resolve the issue, it would be great if you can share the pipeline, so that we could help you better.

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging

Thanks for your help! guys. I’ve already removed the none-ascii character from my folder and it can run. But I still have some troubles.

  1. I used MeasureObjectSizeShape but it calculated parameter of whole image. How can I know the measured parameters of each cells. And also the quantity of the cells

  2. From the result, how can I set the unit(length scale) in the image from pixel to micron as it’s shown on image. so I can recheck the result from program if it correct or not.

This is my pipeline, if you have suggestions, please don’t hesitate to inform me Annotation 2020-02-12 233137

Thankyou :blush:

Hi @Mint_Diabolus,

It looks like your pipeline still needs an export module, such as ExportToSpreadsheet, in order to actually record the measurements somewhere. If you add that you should be able to create a file containing a table for the object measurements.

In CellProfiler all measurements are performed in pixel units. To obtain measurements in microns it’s probably easiest to just multiply the results by whatever the scaling factor is for your microscope setup.

Hi
@Mint_Diabolus

With ImageJ I find 327 elongated particles.

The analysis of the ferrets gives:
Feret Distribution

Hi
@Mint_Diabolus

Use Image J.
To process your image read this: from [30.2 to 30.4]
https://imagej.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.2

Then test this macro:

run("RGB Stack");
run("Stack to Images");
wait(300);
selectWindow("Red");
close("\\Others");
run("Unsharp Mask...", "radius=30 mask=0.60");
wait(300);
//run("Threshold...");
setAutoThreshold("Triangle");
//setThreshold(0, 172);
run("Convert to Mask");
run("Set Measurements...", "area center perimeter feret's add redirect=None decimal=0");
run("Analyze Particles...", "size=1000-Infinity circularity=0.00-0.70 display add");

You get this:

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Hi @Mint_Diabolus,

This is the segmentation that i had got from the CP. It works well. Here it is,

From the MeasureObjectSizeShape module, one of the result MajorAxisLength could be you length of each object.
PFA pipeline. Also have added “ExportToSpreadsheet” module to export your measurements as a seperate CSV file.

TubeStructure.cpproj (654.0 KB)
@bcimini
Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging

1 Like