Common problems with Imview
There are some common problems that are experienced using
imview, mostly under windows. These are:
1. User name includes a space - this will cause a failure to connect with
imview. We will fix this in future Spot updates. Let us know if it is a serious
problem for you.
2. Imview not in your path - imview will fail to start because the installation
process did not update your path correctly (possibly because it wasn't run as
administrator). You can update it manually using the control panel.
3. Imview/R interface requires tcp/ip networking - make sure that this is
enabled on your machine.
The way in which the templates are used and grid finding operates
is often misunderstood.
The idea behind templates is to create one template per batch of
images, not one per image. The template captures information
about offsets between pins, which should remain consistent
among slides printed by the same machine in a given period.
The gridding process attempts to locate the template on an image.
It uses global information and will therefore be likely to fail if you
apply it to a small subset of an array image. It is unlikely to place
the grid in exactly the same place as the template, but it should be
quite close. Technical details are in the user guide.
If you have freedom to set up your experiment you may wish to
consider placement of strongly expressed marker genes in critical
locations (e.g around the edge of the array). This could help make
the grid placement much more reliable and therefore much more
useful in a highly automated procedure. Contact us if you are
interested in this approach.
Slight change to seeded region growing algorithm 25/05/2003
A bug in our implementation of seeded region growing has been
corrected. The problem related to incorrrect assignment of pixels at
the border between two regions. We will add to this page as
common questions/problems arise.
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