Perform the following tasks and edit this file to show your results. Most images you will need are in the images in image_files directory.
You can download FIJI here
A great reference for this assignment is Introduction to Bioimage Analysis by Pete Bankhead.
#Got Help from Chloe_3.5.23
Answer the following questions about the Phase contrast and Differential interference contrast images: Q1) What is the maximum intensity value in the Differential interference contrast file? A1) 254
Q2) What are the dimensions of the Phase contrast file?
A2) (314, 226, 8-bit)
Q3) Which image has greater dynamic range of pixel intensities? Phase or DiffInt?
A3) DiffInt has a higher dynamic range of pixel intensity compared to Phase image
Open the file Fluorescence_composite.tif and convert all the signal in the red channel to the blue channel, export the file as a JPG and upload it to this repository in the image_files directory with the name "Composite.jpg".
The file should automatically show below when uploaded correctly and this file is viewed on GitHub.
Segment the nuclei in the 22946173.tif file and Analyze/Analyze Particles with size (pixel^2) 20–500, Circularity 0.5–1, and Show Count Masks as show in the image below. (Check "Display results", "Clear results", "Summarize", and "Exclude on edges".)
The Results output should look like this:
Save the results as "Results.csv" and upload into the same directory where this file is. It will be used in the Python notebook below.
Also save the resultant "Count Mask" image file with the name "Count_Mask_22946173.tif" and upload into the image_files directory. (It should show up below once it is uploaded).
Q4) How many particles were detected?
A4) 1417
You will do a first-pass assessment of the segmentation output by analyzing the size of the particles using Python...
Open the SizeAnalysis.ipynb file and follow instructions in that file (you will be plotting a histogram of the sizes of the segmented objects and describing the output).