Date: Wed, 1 Dec 1993 08:50:29 -0600 Errors-To: owner-nih-image@soils.umn.edu Reply-To: nih-image@soils.umn.edu Originator: nih-image@soils.umn.edu Sender: nih-image@soils.umn.edu Precedence: bulk From: sarmienu@rnisd0.DNET.roche.com To: Multiple recipients of list 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 (201) 235 3907 Sarmienu@RNISD0.DNET.ROCHE.COM 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 utilitiy 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. --wayne 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: LISTSERV@soils.umn.edu. (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. --wayne