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Installation
Please download all
the files into one folder, on the local machine.
Change the current Matlab directory into the folder
containing the downloaded files. To run the
software, start by directly typing ‘NeuriteIQ_v1’ in
the command window of Matlab. Also, the
Image Process Toolbox of Matlab is required in order
to run NeuriteIQ.
The output of this
software is a Microsoft Excel File. Currently, the
software supports Microsoft Office Excel 2003. If a
higher version of Excel is pre-installed in your
computer, the software may not work properly to
output the correct results.
The third party
software MATITK is used in the released NeuriteIQ.
MATITK is a DLL that makes ITK can be used in Matlab.
The official website of MATITK is as follows.
http://matitk.cs.sfu.ca/
Users can download
the latest version of MATITK directly from the
website, along with the usage guide.
Hardware/Software and image requirement
NeuriteIQ is developed by Matlab of version 7.0, and can only be
executed under the Matlab environment. A Matlab of
version 7.0 or later is suggested to run NeuriteIQ.
NeuriteIQ is designed to deal with neurite image in two different
channels. There is a requirement about memory whose
minimal size should be 1G (2G or larger are
recommended). The maximal image size to be
processed is 2048×2048
pixels, and both of the images length and width
should be the integral multiple of 256 pixels. Since
NeuriteIQ can run at the background without human
interface, there is no strict requirement about the
CPU. As a reference, the average processing time of
a 2048×2048
image is about 10~15 minutes for a PC with a 3.0GHz
CPU.
Manual
·
File
Open
One Image: load single nuclei or neurite image
to display, process, etc.
o
Nuclei channel: load single nuclei image
o
Neurite channel: load single neurite image
Notice:
Corresponding
images of two channels belong to the same well
should be input, so the prefix of their names must
be the same.
Open
One Directory:
load directory of nuclei or neurite images to be
batch processed
o
Nuclei channel: load nuclei image directory
o
Neurite channel: load neurite image directory
Notice:
The number of
images in each channel folder must be equal, and the
sequence of images in both channels must be the
same. Otherwise the program may output wrong
results.
Save
Current Image: save the current displayed figure
as a bitmap image
· Analysis
Single
Processing: automatic labeling and measurement
of cells and neurites for a single fluorescence nuclei or neurite image
o
Nuclei channel: processing single nuclei image
o
Neurite channel: processing single neurite image
Notice:
Single neurite image must be processed after the
corresponding nuclei image being processed.
Batch
Processing: automatic labeling and measurement
of cells and neurites for a fluorescence nuclei or
neurite image database. All the files in the
directory should be .tiff images; results are saved
in an Excel file
o
Neurite channel: batch processing both the nuclei and the neurite
directory
· View
All view functions can be performed by
corresponding buttons in the “View Image Mode”
section.
o
Nuclei channel: view image displayed in nuclei channel
o
Neurite channel: view image displayed in neurite channel
o
Both channel: view image displayed in both channels
·
Edit
Map generation:
will be added later. All view functions has buttons
in the “View Image Mode”.
Enhance: enhance the images displayed in
both channels
o
Nuclei channel: enhance nuclei image
o
Neurite channel: enhance neurite image
Manual Edit:
will be added later
· Help
NeuriteIQ
Help: Users can find details in using the
software in the User Manual v1.0.
Online
Resources: will be added later
Contact:
will be added later
About
NeuriteIQ: version information
Buttons
Nuclei Channel
Setting Range:
Null.
Threshold selection:
Select threshold for enhancing nuclei image.
o
Automatic: system mode
o
Manual: Null. Currently the threshold is selected
automatically by system
Nuclei
Image Mode Selection:
Select different mode of nuclei image after single
processing
o
Raw
Image: display single raw image
o
Boundary: display boundary of cells after single
processing
o
Center Points: display center (seed) points of cells
after single processing
o
Segment Results: display segmentation results after
single processing
96
well: Select “96 well” button before batch
processing if using 96 wells plate
384
well:
Select “384 well” button before batch processing if
using 384 wells plate
View Image Mode
o
Nuclei channel: select “nuclei channel” before using
a function in “View Image Mode”, the function will
be conducted on the nuclei channel only
o
Neurite channel: select “neurite channel” before
using a function in “View Image Mode”, the function
will be conducted on the neurite channel only
o
Both
channels: select “both channels” before using a
function in “View Image Mode”, the function will be
conducted on both channels
o
Scroll bar: the users drag the scroll bar at the
bottom of GUI, and check the images in one or both
channels. The names of displayed images will also
appear under the bar.
o
Zoom
in: zoom in image. Select Nuclei or Neurite channel
before selecting part of image by cursor
o
Zoom
out: zoom out images in both channels
o
Enhance: enhance image. Select Neuclei, Neurite or
both channels before enhancing
Neurite Channel
Setting Range:
Null.
Threshold selection:
Select threshold for enhancing neurite image.
o
Automatic: system default
o
Manual: Null. Currently the threshold is only selected
automatically by system
Nuclei Image Mode Selection:
Select different mode of neurite image after single
processing
o
Raw Image: display single raw image
o
Centerline: display center lines of neurites after single
processing
o
Mask: will be added later
·
Version
Version information of NeuriteIQ
Demos
· Batch process a series of image stacks
File à Open
One Directory
Nuclei Channel
Neurite Channel
Input a value ranged from 5~12 in "Measure"
Analysis àBatch
processing
Nuclei Channel
An excel file contains the labeling and measurement
information of all images in both directory of
database will be automatically generated and saved
in the NeuriteIQ installation directory
· Single process a single nuclei image
File
à Open
One Image
Nuclei Channel
Analysis à Single
Processing
Nuclei Channel
Nuclei Channel Mode Selection
Select different buttons to display single processing results
· Single process a single neurite image
File à
Open
One Image
Neurite Channel
Analysis à Single
Processing
Neurite Channel
Neurite Channel Mode Selection
Select different buttons to display single processing results
Notice:
The single neurite image must be a corresponding image to the nuclei image. Both images must belong to the same well. Single neurite image must be processed after the corresponding nuclei image being processed.
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