Image - Frequently Asked Questions

Download & Installation

Which version should I use?
Generally, the most recent one for your platform. Not everyone likes to upgrade a working version, and a few people can't because of hardware problems, but we don't fix bugs in older versions so it's best to keep to the latest one.
Which platforms are supported?
Currently, binaries are available for Digital OSF, Sun Solaris, SGI and Linux. See question 1.4 for the best way to run image on Intel (Pentium) hardware. We only have Red Hat Linux here, and this is what the Linux version is built with, but it should work with other Linux distributions too. Red Hat changed the system libraries when they released v6, so you need to download the correct version for your Linux release.
Which files do I need to download?
You need the compressed of the latest version tarfile for your platform. Look for the highest version number and the name of your platform in the filename.
Can I run Image on my Windows 95/98/NT computer?
At the moment, the answer to this question is "Yes, so long as you install Linux". Linux is a free Unix for Pentium systems, which can be installed as an alternative to Windows, with a decision made at start-up time which one to run. There may one day be a Windows NT version of Image, and it's possible that this might consent to run under Windows 98, but this will be a largely unsupported activity, and Linux is by far the most stable platform for Pentium users.
Can I run Image on my Macintosh computer?
No, sorry. Macs are just too different from everything else.
Should I ask my system administrators to do the installation?
You can install a copy of Image for personal use without needing to bother your Systems people, but it is better to ask them to install it centrally if it is to be used by more than one person.
How do I configure my installation?
Run the configuration tool supplied as part of the release.
Note: this is only available for version im3.10 and higher.
How do I test my installation?
Download one or more of the test gels from our ftp site, unpack and imimport them, then work through the whole process. Pick a test gel similar to the kind you intend to use locally. You can also try the tutorial .
Image complains it can't find libtiff?
At the moment, you also need the dynamic TIFF Libraries installed on your system (these can be obtained from here) but we hope to include these with the 3.10 distribution so they will no longer have to be obtained and installed separately.

Customising Image for local use

Which scanner should I use?
Image has been tested using gels from a Fluorimager scanner but it should in principle be possible to use any scanner which can produce TIFF image files. You can also analyse gel images from a Macintosh computer attached to an ABI 377 sequencer (see 2.3).
What format should I use for my scanned images?
You should save your gel image in TIFF format. Make sure you scan at a reasonable resolution (one user's problem turned out to be caused by postage stamp sized images which didn't even have as many pixels as there were lanes in the gel) and go for 16-bit (65,535 grey levels). Don't use artists' tools like Photoshop to convert images or change the number of grey levels - pick a suitable scientific image analysis package if you must do this, or you may lose a lot of information in the process.
I'm using an ABI Prism 377 sequencer, how do I transfer my gel images?
The best way is to have the Macintosh on a TCP/IP (not Appletalk) network and install either the free CAP or the commercial Ethershare package on your Unix server. This allows Macs to share the Unix disk and the gel images can be transferred by Dragging and Dropping them. The imimport script will automatically recognise files transferred in this way and do the necessary translations as they are imported. If you can't do this, you may be transfer the gel images with Fetch (a free Macintosh FTP utility) and then turn them into something imimport can work with using the free McVert tools for Unix. Details of how to do this can be obtained from the Support Team, but it isn't anywhere near as good a solution as either CAP or Ethershare.
Why does imimport need to know about projects?
Image uses projects to separate gels of different types. Each project has its own set of defaults, which are inherited by each gel imported into it, so you should use different projects for gels of different types, otherwise you will have to manually set the correct values for each gel. Another reason for having projects is that the supplied imtransfer script will copy results from an Image project into a similarly named FPC project, so you may also want to divide up your gels according to the fingerprinting project they belong to.
How do I make my own standards file?
The standard file is just a text file so you can create it with your favourite editor.
Why does Image complain it can't find a geltraining file?
These are only used by the old, amStep2 lanetracker. Pathfinder, the default, supported lanetracker, doesn't use them at all. From v3.10, BSTT (the Band Shape Training Tool) will no longer be supplied with Image, although Image will still load an old geltraining file if it exists and will use it if configured to use the amStep2 lanetracker. If you don't provide a geltraining file then Image will fall back on internal defaults and inform you that it has done so, but this can be safely ignored if you are using Pathfinder (the default in the distributed version).
What gel layouts can Image use?
Image normalises the mobilities of the standard bands on the gel being analysed to those of the master gel used to create the standards file, and then uses these to normalise the mobilities of the bands in the sample lanes. In order to do this accurately (FPC depends on this) the sample lanes have to have standards lanes on both sides of them. An acceptable gel format thus has standards lanes in the first and last lanes, with sample lanes in between. For greater accuracy, standards lanes should be included uniformly across the whole width of the gel in a regular pattern, so a small gel with 13 lanes might have standards in lanes 1, 5, 9 and 13 with 3 sample lanes in between each pair of marker lanes. Don't economise too much on marker lanes - if you space them too widely and your gels don't run uniformly across their width then Image won't be able to compensate for this and FPC may draw erroneous conclusions from the badly normalised results.
If you are using an ABI Prism 377 sequencer, you can put up to 4 samples in each lane, labelling each with a different dye. One sample in each lane should be the standard, and it should always be labelled with the same dye.
I have 5000 gels already which don't follow the layout rules - can I use them anyway?
As noted above, Image can only analyse samples which are run between lanes containing standards so, depending on the layout of your gels, you may be able to analyse some of the sample lanes. If you have omitted the right hand marker lane, for example, you can tell Image that there are fewer lanes on the gel than there really are, and analyse all but those to the right of the last standard lane. If you only have a single marker lane on the gel, or have a non-uniform arrangement of marker lanes, then there isn't much you can do to salvage them and they will have to be repeated in a format Image can use.
Why does Image complain it can't fetch externally generated clone names with script imclonenames?
In the default configuration Image wil try to use this script to generate clone names, if the script can't be found Image will produce this message. This only a warning message, you can enter the names manually or Image can generate the names automatically based on whatever you entered in the 'first clone name' box on the Gel Parameters dialog. If you want to stop Image trying to call imclonenames you can configure the im3 binary.

Analysing gels with Image

Why does Image crash with an "assertion failed" message when I try to move to the next Step?
there are two possible reasons for this.
  • You are not following the conventions that Image expects each gel to obey. In particular the lane number and/or marker repeat are such that the last lane is not a marker lane. You need to go back to Step0 and fix the parameters for this gel.

    Note: This will mean that you loose any lanes/bands you have already generated.

  • Sometimes Image cannot save some of it's files, maybe there was a network clitch or your disk was full. This can result in inconsistencies between what image expects and the data in the files. You should delete the old files and re-process the gel.

How do I transfer my results to FPC?
The script imtransfer transferes the finished gel to FPC. A version of this script is included in the release of image altough you may need to configure image to use it.
What about the sizes file, can I transfer that too?
you will need to edit the imtransfer script to transfer the sizes file too.
FPC doesn't find any matches between clones on different gels, why is this?
No answer
I'm fed up with typing in the names of my clones every time, can this be automated?
you can configure image to use a script to read the clone names.
Image calls too many bands in every lane, can I restrict it in any way?
You should check that you have set the band height model correctly for your gel type.

Miscellaneous

I think I've found a bug, how do I report it?
just email: image@sanger.ac.uk with the details. Please include the following if available
  • what you were doing when the problem occurred
  • any error messages produced by image either in pop-up windows or in the window from which image was started
  • what type of gel you are trying to process
  • details of the machine on which you are running image, including the version of the operating system
The more information you provide the easier it is for us to track down and fix the bug.
* quick link - http://q.sanger.ac.uk/8k8s4plg