Measuring ''A. thaliana'' Phenotype using FIJI: Difference between revisions
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Protocol: Analyzing Sample Area with ImageJ | '''Protocol: Analyzing Sample Area with ImageJ.''' Written by Rina Rosnow, edited and updated by Hanae Togami, and edited by Hope Ebert (Photos of A. thaliana and related results added by Hope). | ||
Written by Rina Rosnow, edited and updated by Hanae Togami | |||
#Open ImageJ | #Open ImageJ | ||
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###If the scale bar is the same length in all of your images, check ‘global’ to apply scale bar length to all images | ###If the scale bar is the same length in all of your images, check ‘global’ to apply scale bar length to all images | ||
###Click ‘okay’ | ###Click ‘okay’ | ||
#Set measurements | |||
##Go to analyze > set measurements | |||
##Select ‘area’ | |||
##Select ‘limit to threshold’ | |||
##Click ‘okay’ | |||
#Adjust brightness and contrast | |||
##Go to image > adjust > brightness/contrast (or ctrl+shift+c) | |||
##Use slide bars to adjust image to desired appearance (you want the background as dark as possible without obscuring the edges of the sample) | |||
##Click ‘apply’ | |||
#Make image binary | |||
##Go to image > type | |||
##Select ‘8 bit’ | |||
##Go to process > binary | |||
##Select ‘make binary’ | |||
#Adjust threshold | |||
##Go to image > adjust > threshold (or ctrl+shift+t) | |||
##Select Over/Under in dropdown menu and check ‘dark background’ | |||
##Use slide bars to select images/remove background | |||
###Put upper limit to max (bottom slide bar) | |||
###Adjust lower limit using top slide bar | |||
##Click ‘apply’ | |||
#Measure image | |||
##Select ‘wand’ tool in tool bar | |||
##Click anywhere inside the sample to select the sample | |||
##Go to analyze > measure (or ctrl+m) | |||
#Record measurements in the master log | |||
#Save ImageJ image in dated folder | |||
##Select file > save as | |||
##Select ‘tiff’ | |||
##Save image as “GenX_mmddyy_GrowBoxID” |
Latest revision as of 12:57, 16 December 2022
Protocol: Analyzing Sample Area with ImageJ. Written by Rina Rosnow, edited and updated by Hanae Togami, and edited by Hope Ebert (Photos of A. thaliana and related results added by Hope).
- Open ImageJ
- Open image file
- Go to file > open
- Select desired image
- Set scale
- Zoom into scale bar on the original image
- Select ‘linear selecting tool’ on scale bar
- Draw a line along the length of the scale bar on the image by clicking and dragging
- Go to analyze > set scale
- Enter known distance and units
- If the scale bar is the same length in all of your images, check ‘global’ to apply scale bar length to all images
- Click ‘okay’
- Set measurements
- Go to analyze > set measurements
- Select ‘area’
- Select ‘limit to threshold’
- Click ‘okay’
- Adjust brightness and contrast
- Go to image > adjust > brightness/contrast (or ctrl+shift+c)
- Use slide bars to adjust image to desired appearance (you want the background as dark as possible without obscuring the edges of the sample)
- Click ‘apply’
- Make image binary
- Go to image > type
- Select ‘8 bit’
- Go to process > binary
- Select ‘make binary’
- Adjust threshold
- Go to image > adjust > threshold (or ctrl+shift+t)
- Select Over/Under in dropdown menu and check ‘dark background’
- Use slide bars to select images/remove background
- Put upper limit to max (bottom slide bar)
- Adjust lower limit using top slide bar
- Click ‘apply’
- Measure image
- Select ‘wand’ tool in tool bar
- Click anywhere inside the sample to select the sample
- Go to analyze > measure (or ctrl+m)
- Record measurements in the master log
- Save ImageJ image in dated folder
- Select file > save as
- Select ‘tiff’
- Save image as “GenX_mmddyy_GrowBoxID”