Encyclopedia of Graphics File Formats Companion/GFF_CD.ISO/software/mac/nihimage/faq.txt

Internet Message Format | 1994-06-20 | 8.6 KB

Date: Wed, 1 Dec 1993 08:50:29 -0600
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To: Multiple recipients of list <[e-mail]> Subject: Frequently asked questions
X-Listprocessor-Version: 6.0 -- ListProcessor by Anastasios Kotsikonas X-Comment: NIH Image Distribution List

Here are some 11 frequently asked questions with their answers.
These were compiled from recent exchanges in the list. The
authors of the answers are not properly acknowledged (sorry!)
because often the answers are mixes of several answers.

I would like to suggests that this message be sent to people
subscribing to the list for the first time...

--how about it, list administrator?

Juan I. Sarmiento
Department of Toxicology and Pathology
Hoffmann-La Roche, INC.
340 Kingsland street
Nutley, NJ 07110
[phone]
[e-mail]


1. Is there a PC version of Image


Sorry, Image as written makes heavy use of code in the Macintosh
ROM, which is copyright by Apple and cannot be used on non-
Apple hardware. It might be possible to convert it to run
under Windows (with quite a lot of work) but I have not heard
of anyone working on that. The Pascal source is available.
It includes a few routines coded in 68000 machine language
(i.e. hexadecimal code that the 80386 would not understand).
You may want to look into Data Translation "Global lab image"
software. Data translation also sells the hardware (video
capturing cards) and they may come to your place to give
you a demo. Look at page 69 of the Image 1.47 manual for
further information on this system. There is a public domain
version of NCSA Image which is supposed to run on the PC but
I've not tried it. The FTP site address to try is:


ftp.ncsa.uiuc.edu

You can use FTP get copies from there for the PC.

2. I am thinking about purchasing a 660av to use NIH Image
and was wondering about the quality of screen capture.
What file type is it? What is the frame rate for a 640x400
capture? Is the 660av a poorman's viable alternative to
a frame grabber card?

The image capture application that comes with the av Macs
creates QuickTime movies. It is probably no more than 5-10
frames per second and would depend if you are capturing to RAM
or disk. Like the Video Spigot, it's good if you wan't to hook
up a camcorder to your Mac and make a color QuickTime movie.
(The av Macs use the same chip set as the Video Spigot.) You
can convert the QuickTime movie into PICS format to get it
into NIH Image. Wayne has planes to add support for av Macs
in NIH Image. Actually, theys don't work directly (using the
internal a/d video hardware. But, if you use the Video Monitor
control panel with a ccd e.g. a Sony xc77ce-50hz pal camera)
you can import into Image for subsequent processing.


3. Can NIH Image capture images from flat bed scanners?

Many scanner work well with Image via the supplied PhotoShop
plug-in to grab images directly into Image.

4. What are "plug-ins?

Images may be captured from some not directly supported grabbers
via often supplied PhotoShop plug-ins (e.g. a Photoshop plug-in
comes with the Radius VideoVision video grabber). NIH Image
only supports Photoshop plug-ins. The Photoshop plug-ins
developer's kit is available by anonymous ftp from
zippy.nimh.nih.gov, in the /pub/nih-image/plug-ins directory.

5. I am receiving E-mail in BinHex format and don't have the
utilities to decode this type of message. I need to know what
type of utility I need (BinHex 4.0??) and where to obtain it.

Stuffit, a utility commonly available as a public domain in
many electronic bulletin boards may be used to transform files
from binary to hex or viceversa. BinHex can be downloaded
from boombox.micro.umn.edu in /pub/BinHex (Mac ver 4.0 and PC
flavors), wuarchive.wustl.edu (a mirror of sumex-aim.stanford.edu's
macarchives) from directory /mirrors/infomac/utilities
(Mac ver.4.0,5.0). The Mac E-mail program "Eudora", that includes
a BinHex utility for on the fly encoding/decoding, is available
in the sub-directory "communications". If in the future
you need to locate other files available by anonymous FTP there
is a Mac "Archie"-client, Archie 0.9b, available in the
communications directory also. You may need to pick up
"StuffIt Expander" to decode-decompress these downloads from the
"compression" sub-directory and the latest anti-virus utility
updates from "anti-virus". There is a new one going around.

6. We may have a chance to purchase a computer to run NIH Image.
What would be the best board to have for digitizing images
[we find QuickCapture slow and inflexible due to no gain control]?

The Scion LG-3 has software gain and offset control but is not
any faster the QuickCapture card. Both the LG-3 and QuickCapture
are noticabley faster on Macs using built-in video because of
the faster data path to video RAM.

7. Does anybody have suggestions for fast and cheap storage
both on removable disk and tape?

128MB magneto optical disk drives and DAT tape drives have
become very popular here at NIH.

8. Is there a way to get 24-bit colour images into IMAGE? I can
get IMAGE to import the files, but they come out looking pretty
weird (too wide, they repeat on a 3 pixel pattern and look
sheared). If it is possible to make an 8-bit composite or
separate the data into the three colour bands, that would be
great. Is there a way to determine the size of any file-header
offset?

Your images look sheared because you have picked the wrong
width or header size. It is possible to load images without
prior knowledge but it can take a few (read many) tries
before you unwrap them right. There is a macro which
will import 24 bit TIFF from photoshop, it needs to know
the image size (x,y) in pixels. I have found that
this can be a bit tricky to get right. Once you get this right,
NIH-Image will display an 8 bit indexed colour version of your
image. You also get a 3 plane RGB stack, which you can analyse as 3
grey images using macros, and consolidate the results to do colour
analysis. To determine the header size is easy.

Method 1. Read the manual for the application which produces
your images, it should tell you what the header size is.

Or 2. Save an image, as TIFF, uncompressed,of a known size,
containing only black or white. Look at the file size in
the finder, (get info). Subtract the size of the file
(x times y times 3 ) for the image from the total file size,
which should leave the header as a remainder.

Or 3. Use a file editor such as the renowned FEDIT (is my
age showing here?) or similar, which will allow the display
of the data in a file, and read the x, y image size as the
first few bytes in the header for TIFF images. Then look
through the file until you find image data (hence the
reason for black or white images) the values should be 00 or
FF. Count the bytes from the start of the file to the start
of the image and that is the header size. Try these numbers in
the Import, which should open up the image as a three times
as wide image without shearing. Then go to work on
your own macro based on the one used to import photoshop
images, so that the pixels for each colour plane are put into
the appropriate layer in a three layer stack


9. How can I use Image to read DNA sequencing gels?


- Set the x-y center in the options dialogue box under the analyze
menu.
- Select the area of interest with the polygonal tool. Make sure
you select the A, C, G, and T lanes.
- Threshold the image to select bands by their grey level.
- Select Analyze particles from the analyze menu.
- Show results and option copy.
- Go to EXCEL and paste.
- Sort the table by the X values.
- Create a new column and enter the base (ACGT) according
to the approximate vertical center of the location of
the corresponding lane.
- Sort the table by the y values.

10. Subject: Re: unsibscribe NIH-IMAGE

Unsuscribe messages should be sent to:
[e-mail]. (they also need to be spelled correctly :-).

11. Can anyone give me some insight on importing 32 bit data?

The current version of NIH Image (1.52) cannot import either integer
or real 32-bit data, but this is something that is on my list of
things to do. IPLab (Signal Analytics, 703-281-3277) should be
able to import 32-bit data since it supports both integer and
real image data types.