Measuring ''A. thaliana'' Phenotype using FIJI by Hand: Difference between revisions
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PreDec2022>MSmith9 (Created page with "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 l...") |
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Open 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). | ||
Open image file | |||
Go to file > open | #Open ImageJ | ||
Select desired image | ##Open image file | ||
Set scale | ##Go to file > open | ||
Zoom into scale bar on the original image | ##Select desired image | ||
Select ‘linear selecting tool’ on scale bar | #Set scale | ||
Draw a line along the length of the scale bar on the image by clicking and dragging | ##Zoom into scale bar on the original image | ||
Go to analyze > set scale | ##Select ‘linear selecting tool’ on scale bar | ||
Enter known distance and units | ##Draw a line along the length of the scale bar on the image by clicking and dragging | ||
If the scale bar is the same length in all of your images, check ‘global’ to apply scale bar length to all images | ##Go to analyze > set scale | ||
Click ‘okay’ | ###Enter known distance and units | ||
Set measurements | ###If the scale bar is the same length in all of your images, check ‘global’ to apply scale bar length to all images | ||
Go to analyze > set measurements | ###Click ‘okay’ | ||
Select ‘area’ | #Set measurements | ||
Select ‘limit to threshold’ | ##Go to analyze > set measurements | ||
Click ‘okay’ | ##Select ‘area’ | ||
Adjust brightness and contrast | ##Select ‘limit to threshold’ | ||
Go to image > adjust > brightness/contrast (or ctrl+shift+c) | ##Click ‘okay’ | ||
Use slide bars to adjust image to desired appearance (you want the background as dark as possible without obscuring the edges of the sample) | #Adjust brightness and contrast | ||
Click ‘apply’ | ##Go to image > adjust > brightness/contrast (or ctrl+shift+c) | ||
Make image binary | ##Use slide bars to adjust image to desired appearance (you want the background as dark as possible without obscuring the edges of the sample) | ||
Go to image > type | ##Click ‘apply’ | ||
Select ‘8 bit’ | #Make image binary | ||
Go to process > binary | ##Go to image > type | ||
Select ‘make binary’ | ##Select ‘8 bit’ | ||
Adjust threshold | ##Go to process > binary | ||
Go to image > adjust > threshold (or ctrl+shift+t) | ##Select ‘make binary’ | ||
Select Over/Under in dropdown menu and check ‘dark background’ | #Adjust threshold | ||
Use slide bars to select images/remove background | ##Go to image > adjust > threshold (or ctrl+shift+t) | ||
Put upper limit to max (bottom slide bar) | ##Select Over/Under in dropdown menu and check ‘dark background’ | ||
Adjust lower limit using top slide bar | ##Use slide bars to select images/remove background | ||
Click ‘apply’ | ###Put upper limit to max (bottom slide bar) | ||
Measure image | ###Adjust lower limit using top slide bar | ||
Select ‘wand’ tool in tool bar | ##Click ‘apply’ | ||
Click anywhere inside the sample to select the sample | #Measure image | ||
Go to analyze > measure (or ctrl+m) | ##Select ‘wand’ tool in tool bar | ||
Record measurements in the master log | ##Click anywhere inside the sample to select the sample | ||
Save ImageJ image in dated folder | ##Go to analyze > measure (or ctrl+m) | ||
Select file > save as | #Record measurements in the master log | ||
Select ‘tiff’ | #Save ImageJ image in dated folder | ||
Save image as | ##Select file > save as | ||
##Select ‘tiff’ | |||
##Save image as “GenX_mmddyy_GrowBoxID” |
Revision as of 14:31, 26 July 2021
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”