Measuring ''A. thaliana'' Phenotype using FIJI by Hand

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