Frequently Asked Questions

* Is there an NIH Image Home Page?
* How do I download NIH Image using a Web browser? 
* How do I download NIH Image via FTP?
* How do I (un)subscribe to the NIH Image mailing list? 
* Is there a way to search posts for an answer to my questions? 
* How do I post a question on the NIH Image mailing list? 
* I don't want a ton of email but I want to subscribe, how? 
* Does NIH Image run on a PC?
* Is there a UNIX version of NIH Image?
* How can I allocate more memory to NIH Image? 
* Why does the desktop change color when I run NIH Image? 
* Why does text look ragged when I print on a laser printer? 
* How can I get black to be 0 and white 255? 
* Why does the Paste command sometimes get dimmed out? 
* How can I create a composite color image? 
* How can I convert a stack to a QuickTime movie? * How should I cite NIH Image?
* Is there any help in understanding densitometry and/or gel analysis? 
* Can I modify NIH Image?

--------------------------------------------------------------- 
* Is there an NIH Image Home Page?

The NIH Image home page provides on-line documentation, links to download the software, tutorials, links to other image processing software, an archive to search for answers to questions and more. The NIH Image home page is located at:

http://rsb.info.nih.gov/nih-image/

--------------------------------------------------------------- 
* How do I download NIH Image using a Web browser? 

The latest version of NIH Image, documentation, source code, macros and more can be downloaded by going to NIH Image Home Page and following the "Download" link.

--------------------------------------------------------------- 
* How do I download NIH Image via FTP?

The latest version of NIH Image, documentation, source code, macros and more can be found on the anonymous ftp server zippy.nimh.nih.gov. Choose the directory directory /pub/nih-image. The best way to download the program is to use the user-friendly Macintosh FTP client Fetch. 

--------------------------------------------------------------- 
* How do I (un)subscribe to the NIH Image mailing list? 

The NIH Image mailing list is a forum to post and answer questions concerning NIH Image and its use. There are over a thousand subscribers to the list. Subscription and all mail routing is done via a listproc server at the University of Minnesota. Subscribe to the NIH Image mailing list by sending a message containing the line:

subscribe nih-image [your real name]

Note: substitute subscribe or unsubscribe as appropriate Send this message to listproc@soils.umn.edu There is a separate email address (nih-image@soils.umn.edu) for posting your question or answer regarding NIH Image.
--------------------------------------------------------------- 
* Is there a way to search posts for an answer to my questions? 

Hundreds of questions about NIH Image have been asked and answered on the NIH Image mailing list, which is subscribed to by over 1000 NIH Image users. You can see if your question has come up on the list by doing a keyword search of the list archives at:

gopher://gopher.soils.umn.edu

Note: you can narrow searches by combining keywords using AND. 

You can also browse the monthly list archives at: 

http://www.soils.agri.umn.edu/infoserv/lists/nih-image/archives/ 

If you can't get an answer by searching the archives, try posting a message to the list.

--------------------------------------------------------------- 
* How do I post a question on the NIH Image mailing list? 

Send a message to the list (you must be subscribed) at the address: 

nih-image@soils.umn.edu

Your message will be routed to each and every person on the list. You should, therefore, consider the nature of your post and by all means do not send email subscription requests to this address. --------------------------------------------------------------- 
* I don't want a ton of email but I want to subscribe, how? 

You can set your subscription to "digest" mode, which collects all the daily messages (sometimes there will be very many) and sends it out once per day. Send an email message to listproc@soils.umn.edu with the command: 

set nih-image mail digest

To reset your subscription to "trickle", or many mailings mode send: 
set nih-image mail ack

--------------------------------------------------------------- 
* Does NIH Image run on a PC?

Scion Corporation is porting NIH Image to Windows 95. See the "What's New?" section of the NIH Image home page for more information. NIH Image also runs under DOS, Linux, or NextStep using the Executor Mac emulator from Ardi 

(http://www.ardi.com).

--------------------------------------------------------------- 
* Is there a UNIX version of NIH Image?

NIH Image has not been ported to UNIX but it runs on SUN and HP workstations using Apple's Mac emulator for UNIX called Macintosh Application Environment (MAE). Information about MAE is available from "http://www.mae.apple.com".

--------------------------------------------------------------- 
* How can I allocate more memory to NIH Image? 

or: My Mac has 128MB of RAM but the NIH Image About Box shows only 2500K free. Why is that?

You need to allocate more memory to NIH Image. Click (once) on the NIH Image icon (a microscope), select the Finder's Get Info command, and increase "Preferred size".

--------------------------------------------------------------- 
* Why does the desktop change color when I run NIH Image? 

NIH Image uses all but two of the 256 available screen colors when the monitor is set to 256 colors. The two "colors" that Image never changes are white (0) and black (255). Objects on the screen that are not black and white are likely to change color when NIH Image is being used. You can avoid this problem by selecting "Desktop Friendly" in Preferences, but this reduces the number of grays displayed to 16. If your hardware supports it, you can also avoid this problem by switching the monitor to "thousands" or "millions" of colors.

--------------------------------------------------------------- 
* Why does text look ragged when I print on a laser printer? 

NIH Image treats text as if it were part of the bitmapped image. To create high quality text for laser printer output and slide makers you need to export the image to a multi-layer, object-oriented drawing program, such as ClarisDraw or PowerPoint.

--------------------------------------------------------------- 
* How can I get black to be 0 and white 255? 

or: In NIH Image, white is 0 and black is 255, which is the opposite of what I'm used to. How can I change this? 

Check "Invert Pixel Values" in Preferences. This sets up an inverting density calibration function, causing pixels values displayed in the Info and Results windows to be inverted.

--------------------------------------------------------------- 
* Why does the Paste command sometimes get dimmed out? 

Images copied to the clipboard are stored in the Clipboard buffer. In some situations, such as filtering, NIH Image has to use the Clipboard buffer for internal operations. When this is happens, the Paste command gets dimmed out.

--------------------------------------------------------------- 
* How can I create a composite color image? 

You can't normally combine two images that have different LUTs, but if you check "Keep LUT" when you open the second image (which must be stored as a PICT file) its pixel values will be remapped to conform to the LUT of the first image. You will then be able to successfully Copy and Paste, since both images have the same LUT.

--------------------------------------------------------------- 
* How can I convert a stack to a QuickTime movie? 

Use the Save As command and select QuickTime.

--------------------------------------------------------------- 
* How should I cite NIH Image?

Published research assisted by NIH Image should use a statement similar to the following in the materials and methods section "... analysis performed on a Macintosh computer using the public domain NIH Image program (developed at the U.S. National Institutes of Health and available on the Internet at http://rsb.info.nih.gov/nih-image/)". 

--------------------------------------------------------------- 
* Is there any help in understanding densitometry and/or gel analysis? 

There are a number of documents available explaning anything from portions of the theoretical prinicples of densitomtry, to step by step help in using the gel analysis macros. Those interested in densitometry should strive to understand the "calibrate" command and why it is used. 

For explanation regarding basic underlying principles of densitometry read the section of Image Engineering on densitometry at: http://rsb.info.nih.gov/nih-image/Engineering/ImgEngr.html#densitometry 

For simple explanation on the calibrate command, the NIH Image manual section should be read:
http://rsb.info.nih.gov/nih-image/manual/menus/analyze.html#calibrate 

For basic step by step explanation on the gel macros the NIH Image manual, techniques section, section should be read: http://rsb.info.nih.gov/nih-image/manual/tech.html#analyze 

For a longer and thorough step by step explanation as to how to use the gel macros refer to the gel analysis manual at: http://sunny.dcrt.nih.gov/itc/gel/

Calibrated optical density step tablets are made by Kodak and can be purchased from Kodak dealers. See Kodak's step table Web page at 

http://www.kodak.com/aboutKodak/bu/dai/SIS/stepTab.shtml 

--------------------------------------------------------------- 
* How can I modify NIH Image?

There are two ways to modify NIH Image: a macro (with relative ease) or the pascal source code. The NIH Image manual can help getting you started on macros. If you opt for pascal source code modifications you will need the Metrowerks Codewarrior compiler to make source modifications and recompilation. You might also look at the manual entitled Inside NIH Image for additional help in macro and pascal modifications and why you might choose either option.