RootflowRT v.2.8
Imaging
for RootflowRT v.2.8
Input
Image Requirements
Images
should be in .tif or .ppm
format, contain 8-bit gray scale values and 640x480up to 1200x1600 in dimension.
Roots are imaged as overlapping stacks of image frames throughout the tip to the maturation
zone or as a single stack of just one region such as the root tip. Overlapping
between stacks should be at least 20% of the field of view. Each image stack
must contain 9 frames or images such that every frame in a stack is taken at precise time intervals as choosen by the user.
Input
Image File Names
The
software expects the image files to be named according to precise conventions.
In particular, the images should be named Stack00xxFrame00yy with or without
filename extension such as .tif or .ppm. For example, a root may be imaged with 5 overlapping
stacks with frames taken every 15s. In this case, the image files can be:
Stack0001Frame0001.tif
Stack0001Frame0002.tif
.
.
Stack0003Frame0001.tif
.
.
Stack0005Frame0009.tif
Mosaic
Method Between Overlapping Stacks
This
refers to the process of blending together the velocity profiles of each of the
individual stacks into one complete velocity profile for the entire root. There
are two ways this can be executed:
1)
Moving a precise fixed distance between every stack with an
inchworm device such as provided by EXFO Burleigh
Products Group, Inc.
2)
Taking a highly textured image of the background after the 9th
frame and naming it Stack00xxBack 0001 eg.Stack0006Back 0001.tif. At this time,
the space in the filename is required. If you are imaging on agar plates, the
use of graphite or sand very near, but not on the root throughout the imaged
region is desirable.
Image
Quality
The
software’s ability to make accurate motion estimation is integrally dependent
on image quality. Good images have a histogram that is spread out and there is
good focus throughout the root.
Fairly Good Root Image:
Motion Mask Image
Resulting Velocity Profile
Very Poor Root Image:
Motion Mask Image
Resulting Velocity Profile
