Hippocampal neuron quantification

Thank you Laksshmi for your help!!
Fancy.

Hi Lakshmi,
Do you know whether the ‘Mean_MaskedNeurons_AreaShape_Area’ in the output file is the total area of masked region? The online mannual says it is the pixel, but the number I got is ‘59’, seems pretty small. I want to calculate cell number/mm2 if possible.
Thank you.

Hi Fancy,

Just to be sure, this the mean Area of the all the Neurons inside the mask(s) for the complete image (per image information). This is the mean area of the Masked Neurons. Generally, Cellprofiler gives values in pixels, the conversion scale you could do it based on your image. You may also want to check this reply,

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
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Hi Lakshmi,
You mean that is the area of all neurons within the mask? Is there a way to measure the size of the masked area? I want to present it as number/area so need to measure the masked area.
Thanks for the pixel conversion info.

Hi Fancy,
Yes, it is the area of all neurons within the mask.
To compute size of the masked area, you can add this mask as another object in “MeasureObjectSizeShape” module as shown in the screenshot.

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
Join us at the High Content Analysis Symposium Oct 21-22, London

Society for Laboratory Automation and Screening

SLAS 2019 Advanced 3D Human Models and High-Content Analysis Symposium

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

Hi Lakshmi,
I added this module and ‘CalculateMath’ to convert the unit from pixel to mm2. For masked area, is it in MyExpt_mask.csv file, which column should I look at? “AreaShape_Area” or “Math_Measurement”? Am I using the right pipelines in the right order? Thank you very much!
image
image

Hi Fancy,

You are right!!!To be more clear, you could rename the “Name the output measurement”. For me your pipeline looks fine…

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
Join us at the High Content Analysis Symposium Oct 21-22, London

Society for Laboratory Automation and Screening

SLAS 2019 Advanced 3D Human Models and High-Content Analysis Symposium

Read more on our site.

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

Hi Lakshmi,
I have one more question. So for the images I used 4X or 20X in microscope, how should I account for that in CP? Now I am just using the area (in pixels) from CP and calculate into mm2, I am not sure if I need to indicate different magnitude (4X or 20X) in CP setting somewhere?
Thank you!

Hi Fancy,

You need not specify your magnitute anywhere in CP. As I had mentioned before, CP alsways gives you in pixel unit. The other unit conversion according to your requirement, you might have to do it and this would be based on your image scale for example 1 pixel = 0.5micron.

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

Join us at the High Content Analysis Symposium Oct 21-22, London
Society for Laboratory Automation and Screening

SLAS 2019 Advanced 3D Human Models and High-Content Analysis Symposium

Read more on our site.

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