The units of variables are pixels?

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The units of variables are pixels?

Post  arife on Tue Oct 12, 2010 10:11 am

Dear all,

I am trying to manipulate the data (.txt file from the pid_process/pid_results/Dat_1validated folder ) by using the Short Manual from the webpage. There, it says that 1 pixel is equal to 10,5833 microns (if the resolution is 2400). I understood from here that all the variables in the .txt file are given in pixels; and to manipulate them in the EXCEL we have to convert them, am I right?

Thank you,
Best regards,

Arife Z.Yılmaz

arife

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Re: The units of variables are pixels?

Post  Carmen Garcia-Comas on Thu Dec 16, 2010 11:17 am

Hi Arife,

Yes, the measurements correspond to pixels:

Milimeter/1pixel=25.4/Resol*1000)*10-3 (if Resol=2400; 10.5833 microns/pixel);
So the values of “Area” column have to be transformed by multiplying it (e.g. for 2400 resolution: Area*10.58332 (because the area is in 2 D), and Major=Major*10.5833.

Maybe this short manual could help you with your analyses:

http://www.obs-vlfr.fr/LOV/ZooPart/ZooScan/Download%20Softwares/ZooProcess/ZOOSCAN_ShortUserManual.pdf

Good luck
Carmen

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Re: The units of variables are pixels?

Post  arife on Thu Dec 16, 2010 6:04 pm

thankyou

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Re: The units of variables are pixels?

Post  Carmen Garcia-Comas on Mon Dec 20, 2010 10:38 am

ok, I helped a girl working with excel once.
You open you txt files with excel (; separator)
and the column variables of interest are:
Area (column C), Major (column R), Minor (column S), pred_valid_Id (name of organism)(last column, i.e., BU)

Area_mm2 =C2*10.5833*10.5833*(10^(-6)) (formula for all the column)

ESD volume in mm3=(4/3)*3.1416*((Area_mm2/3.1416)^(3/2)) (for all the column)

Major mm =R2*10.5833*0.001 (for all the column)

Minor mm: S2*10.5833*0.001 (for all the column)

EllipsoidalVol(mm3): =(4/3)*3.1416*(Major mm/2)*(Minor mm/2)*(Minor mm/2)(for all the column)

then do a histogram of your data by sorting them in size classes previously established depending on the size limits of your data (and each class is the double of the previous one)
and divide the biovolume contained in each size class by the average volume representing the size class and represent the spectra by their log2.

cheers
Carmen

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