Perineuronal net Intensity Program for the Standardization and Quantification of ECM Analysis
For description of protocol, see:
Please cite Slaker, Harkness, and Sorg (2016) when using the PIPSQUEAK macro. (PDF here.)
- Slaker M, Harkness JH, and Sorg BA. A standardized and automated method of perineuronal net analysis using Wisteria floribunda agglutinin staining intensity, IBRO Reports, 2016
You can download PIPSQUEAK from ImageJ by adding our repository to your FIJI Update Sites.
Thank you for support from:
Washington State University
WSU Postdoctoral ADARP Grant
WSU Office of Commercialization Gap Fund
Rewire Neuroscience, LLC
To install the macro:
PIPSQUEAK can be run on either FIJI or ImageJ, but to receive automatic updates to the macro, you must use FIJI and add PIPSQUEAK to your FIJI Update Sites. To do this, follow the instructions below. To use ImageJ, you will have to download and install PIPSQUEAK manually.
Open FIJI (or download it here: http://imagej.net/Fiji/Downloads ).
Once FIJI is installed and opened, go to Help > Update.
Then, click Manage Update Sites
Then, click Add Update Site
In the center field, enter: http://sites.imagej.net/PIPSQUEAK/
In the “Hosts” column, enter: webdav:PIPSQUEAK
Then, click Close
Then, click Advanced
From there, you should see at the top: “PIPSQUEAK.txt”
Click it and then click Install, and then Apply changes
It will install and prompt you to restart FIJI
After restarting, and go to Plugins > Macros > Install
It should have directed you to the macro folder in FIJI, where you’ll click PIPSQUEAK.txt”
Then the macro should be listed in Plugins > Macros
Every time you restart FIJI you’ll have to reinstall the macro (Plugins > Macros > Install)
If you want it to install automatically on start up, go to Plugins > Macros > Edit, then choose your “AutoRun_Scripts.imj” file. Then:
In FIJI add the lines:
In FIJI add the lines:
run(“Install…”, “install=[LOCATION OF FIJI ON YOUR COMPUTER]/Macros/PIPSQUEAK.txt”);
Save, restart, and enjoy!
About the macro
New! Instructional videos:
Settings, Features, and Setup
Image Scale Determination
0.90 CHANGE LOG: Data log output format revised for easier export. Started logging changes
0.91 CHANGE LOG: Lowered PV pixel detection requirement. Removed Double-label Open Next Functionality. Bugs Squashed
0.92 CHANGE LOG: Splines Reticulated. Llamas Herded.
0.93 CHANGE LOG: Don’t ask about 0.93-0.942
0.943 CHANGE LOG: Lots of good things. Big changes. Re-strategized ROI seeding for double-labeling. Added user choice for ROI enlargement. Started saving ROI overlays in directory. Raw images retained for double-label double checking in semiautomated mode.
0.944 CHANGE LOG: Fix bug in saving single-label ROIs.
0.945 CHANGE LOG: Fix for double-labeled PV user check timing.
0.946 CHANGE LOG: Set default WFA ROI enlargement size to “0”. Added merged image load during double-label check steps.
0.947 CHANGE LOG: Reinstated WFA ROI expansion to prevent ROI withering during double-labeling”
>> 1.00 CHANGE LOG: Nothing changed from 0.947. Future versioning strategy will use the tenths place digit to signify significant changes that will affect analysis results (ie 1.03 to 1.10). Data collected using versions of PIPSQUEAK that differ by a tenths place digit should not be directly compared. Data collected using versions of PIPSQUEAK similar by the tenths place digit can be compared or combined in statistical analysis (ie 1.03 and 1.04 or 1.09).