iPath-Server
telepathology database user’s guide
Kurt Brauchli
iPath-Server: telepathology database user’s guide
by Kurt Brauchli
Copyright © 2001 by K. Brauchli, Dept. of Pathology, University of Basel, Switzerland
This is a very preliminary version of a user’s guide for the telepathology database of the iPath
Internet Pathology project. Any contributions to this work are highly welcome.
Table of Contents
1. Introduction .......................................................................................................................7
2. First Steps with the Telepathology Database ..............................................................9
Requirements ................................................................................................................9
Overview .......................................................................................................................9
Discussion Groups..............................................................................................9
Create a new user account ..........................................................................................9
The main menu for registered users........................................................................10
Options...............................................................................................................11
Navigation and Help .................................................................................................12
Menubar.............................................................................................................12
Toolbar................................................................................................................12
Viewing and commenting cases...............................................................................13
case list ...............................................................................................................13
Case display.......................................................................................................14
Comments..........................................................................................................14
Add new cases ............................................................................................................15
create a new case...............................................................................................15
adding images and other documents ............................................................16
Edit an existing case...................................................................................................17
3. Advanced Functions.......................................................................................................19
Chat ..............................................................................................................................19
Special case options....................................................................................................19
Allow other users to add images....................................................................19
Publish case .......................................................................................................19
Hide comments .................................................................................................19
4. Moderatoration of a Discussion Group......................................................................21
What is a moderator ..................................................................................................21
Exmaple Configurations............................................................................................21
General recommendations ..............................................................................21
Expert to expert consultation..........................................................................21
Many non-experts consulting a few specialists............................................22
Teaching: Setting up a group with a reference atlas ....................................22
Configuration of discussion group ..........................................................................22
Setting the group membership .......................................................................23
5. Administration of an iPath Server...............................................................................25
Bibliography ........................................................................................................................27
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6
Chapter 1. Introduction
This user guide for the iPath Telepathology Database (tpdb) will provide basic information on how to use the tpdb.
The first chapter covers the main aspects for a common user. How to register
with a server, how to view and create cases as well as how to configure your
personal settings. For this section we assume that you have access to an iPath
Telepathology Server. Our main server at the University of Basel can be found at:
http://telepath.patho.unibas.ch 1
Note: This test server is provided as is. No functionality, backups or so is guaranteed.
In a second chapter we will see what you have to do to moderate your own discussion
group.
A last chapter will cover all aspects of administrating an iPath Telepathology Server.
This chapter is aimed at those who want to run their own iPath Server.
Notes
1. http://telepath.patho.unibas.ch
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Chapter 1. Introduction
8
Chapter 2. First Steps with the Telepathology Database
Requirements
The iPath Telepathology Database (tpdb) can be accessed with any common web
browser. Both, Netscape (version 4.75) and Internet Explorer (version 5) have been
tested. On Macintosh Computers Netscape does not run properly with the online
chat and the telemicroscopy facility of the iPath server.
The session management of the database requires cookies to be enabled.
Most browsers will be setup to accept cookies, but if you cannot login
to the database though you enter the correct password, please check if
your browser has cookies enabled. In Netscape you find this option under
Edit/Preferences/Advanced/Accept Cookies. In MSIE you must go to
Extra/Internet Options/Security/Custom Level. Here you can check the enable
cookies option.
To use the full functionality make sure that JavaScript is also enabled. While this is not
mandatory, it is more convenient to work with iPath server if JavaScript is available.
Overview
The Telepathology Database (tpdb) of the iPath Telepathology Server is intended to
serve as a tool for consulations over the internet. It may be used for expert groups
to discuss difficult cases as well as for non-experts to consult a specialist pathologist.
Every discussion takes part in a so called discussion group, a term that should be
explained first.
Discussion Groups
A discussion group is the fundamental unit for using the tpdb. Every group has a
moderator (usually a pathologist) who can grant access to the group to any user resistered on the server.
Once a user is member of a discussion group, he or she can start adding cases to this
discussion group. Every case is stored within a discussion group and is visible only
to other members of the discussion group unless the sender of the case or the group
moderator explicitly publishes the case.
Every case belongs to the user (sender) who entered it into the tpdb. Only the sender
and the group moderator can edit/alter a case. All other members of the discussion
group can only view it. If they want to state their oppinion on a case, they can add a
comment to the case.
Create a new user account
The first thing to do is to register yourself with the iPath Telepathology Server. On the
start page of an iPath Server (e.g. our main server at http://telepath.patho.unibas.ch
1
) you follow the ’registration’ link. On the following registration form you must fill
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Chapter 2. First Steps with the Telepathology Database
out some personal information like name etc. and chose a username and password.
Click the save button to continue.
Figure 2-1. Registration of a new user
If the username you have chosen is already in use, or if you mistyped your password,
you will be asked to correct it. If you have succesfully registered your next step is to
become a member of a discusscion group. Access to discussion groups is provided
by the moderator of the according group, so contact the moderator of your group of
choice. A list of all groups on an iPath Server (incl. their moderator) can be found at
the group list link.
If you want to start a new discussion group please read the chapter on moderating a
discussion group.
The main menu for registered users
Once a user has successfully logged in he is presented his personal start page or main
menu illustrated in the figure above. Under A all discussion groups of the user are
listed. By clicking on the group name, you can access the case list of this group. On
the right side (marked with B) you find other functions and options.
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Chapter 2. First Steps with the Telepathology Database
Figure 2-2. The tpdb main page
Options
This section contains the global configurations and options a user can modify.
Change Password/Personal Information
To change your personal information (address, email) or your password, follow this
link.
Personal settings
There are some global settings a user can change. At present you can chose your
preferred language - English or German at the moment - you can switch on/off the
text in the toolbar and you can set up which discussion group should be used to store
cases when you use the iPath-Microscope application to connect your microscope to
the internet (cf. the iPath-Microscope user guide).
Figure 2-3. personal settings
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Chapter 2. First Steps with the Telepathology Database
Information via email
If you want to be informed when new cases were stored in a discussion group or
when new comments have been added you can use this function to instruct the server
to send you an email. In the following window, check all the events you want to be
informed about an press the save button.
Figure 2-4. Infomation via email
Navigation and Help
Menubar
First some general hints for navigating in the tpdb. On every page there is a navigation bar at the top of the page (cf. Figure 2-5). The two small icons on the very
right are present on every page. The question mark opens a help window which
displays some specific help text for the page that you are just seeing. The logout icon
will close the current session with iPath. You must login again to access data.
Figure 2-5. the tpdb navigation bar
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Chapter 2. First Steps with the Telepathology Database
Toolbar
Most functions of the tpdb are available over a so called toolbar like illustrated in this
figure. The text labels below the icons can be switch on or off by the user in personal
settings. The content of the toolbar may be different on some pages than on others,
as the toolbar is only displaying the functions which are available and permitted at
this place. To find out more about the functions available on each page, click on the
little help icon in the navigation bar.
Figure 2-6. the tpdb toolbar
Viewing and commenting cases
case list
Figure 2-7 shows the case list for one discussion group. The case list is accessed from
the main menu by clicking on the according group name. By default the cases are
sorted by date in an descending order. The newst cases are at the top of the list. The
sort order can be changed by clicking the sort icon
next to the colmn title that
should be used as a sort key.
If there cases is the group that have been entered they after your last login, they are
labeled as new. When a cases comments that have been added since your last login,
it is labeled with a smal red cross
.
To display a single case, click on the case title. If there are too many cases to be displayed on one page, you find a link to the next page at the bottom of the list (cf.
encirceled red in Figure 2-7)
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Chapter 2. First Steps with the Telepathology Database
Figure 2-7. The case list
Case display
Figure 2-8 illustrates the display of a single case. The general information of the case
is displayed at the top of the page followed by the description given by the sender of
the case. Below the description there are all images attached to the case. The images
can be displayd by clicking it. On the image display, there are on the left margin two
arrow icons ( ) to browse through all consecutive images. To go back to the main
case display follow the ’back’ link or use the up-arrow in the navigation bar.
At the bottom of the case display you will find the comments added by other users.
If you see no comments but instead a red label saying "comments hidden" this is a
case with hidden comments. You can only see comments of other users after you have
entered your own comment (cf. next section).
Figure 2-8. Display of a single case int the tpdb
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Chapter 2. First Steps with the Telepathology Database
Comments
Add a new comment
If you want to state your opinion on this case you can add a comment to this case.
Click on the "add comment" link and fill your comment tonto the following form.
When you are finished click on the save button to send your comment to the iPath
server. NOTE: you can only enter comments when you are logged in and you cannot
alter comments once they are saved.
The comments are allways listed in the order they were submitted. The first comments (oldest) stay on top.
Hidden comments
To prevent users from being influenced by comments already stated, comments can
be hidden. In a case with hidden comments you can see comments of other users
only after you have entered and saved your own comment.
Final diagnosis
The moderator of the group and ev. the sender of a case can add a special comment.
Below the textfield to enter the comment, there is a check box labeled final diagnosis.
If this is check before saving the comment, this comment will be put on top of the
comment list and it will be colored red. This is intended for the statement of some
conclusions or a final diagnonsis after the discussion on thie case is finished.
Add new cases
create a new case
Creation of new cases takes two step. First, a new cases is added to the database and
in a second step images can be attached to this new case.
To create a new case click on the "new case" icon in the tool bar. In the following form,
illustrated in Figure 2-9, you must fill out some fields. The case title is mandatory. If
the group moderator has specified a default description text, this will be written in
the description field. Complete the description by overwriting the default values with
the description of your actual case. When you have typed all infomation you save the
case to the tpdb by clicking the save button or the save icon in the tool bar.
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Chapter 2. First Steps with the Telepathology Database
Figure 2-9. Add a new case to the tpdb
adding images and other documents
Images
Once the case is created you can start adding images or other documents (e.g. pdf or
ms-word) to this case. Click on the paper clip icon in the tool bar to open the "add
image"-dialog illustrated in Figure 2-11.
Figure 2-10. Add Image with the "attach" icon
•
first click the "browse" button to open the file selction dialog.
•
In the file selction dialog select an image file that you want to add to the case and
click "open".
•
Finally press the "Save/Preview" button to see a preview of your image and wait a
few seconds until your image is uploaded to the server.
If you are content with the image displayed in the following preview dialog, click
"save" to save the image to the database.
If you cannot see an image in the preview window, this might have several reasons.
There can a maximum upload size on the server (e.g. 2MB per image on our main
server). If an image file is larger it is not uploaded. Another problem can be the image format. The easiest and most convenient way to upload images are JPEG files
compressed with good quality. On the server all other file formats are converted to
JPEG anyway, so there is no reason to send high quality but large TIF files.
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Chapter 2. First Steps with the Telepathology Database
Figure 2-11. Add images or other documents to a case
Other documents
If you want to add another kind of document, ie. not an image file, you can check the
"store as binary file" option in the "add image"-dialog (Figure 2-11).
Edit an existing case
You can edit an existing case only if you have sent in the case yourself or if you are
group moderator. To edit a case click on the edit icon (cf. Figure 2-12).
Figure 2-12. Edit case icon
On the following windows there are three things to edit. Shown under A in Figure
2-13 you can edit the general case description and all the case options.
Under B you can check images that should be removed from this case and under C
you can renumber the images. Images will always appear in ascendending order of
the image number.
When finished with editing, click the save button or the the save icon in the toolbar
to save your changes on the server!
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Chapter 2. First Steps with the Telepathology Database
Figure 2-13. Edit an existing case
Notes
1. http://telepath.patho.unibas.ch
18
Chapter 3. Advanced Functions
Chat
The chat function is intended to allow an onlie discussion between two or more members of a discussion group. For every case there is a private chat room. To join the chat
room, go to the appropriate case and click on the chat icon (cf. Figure 3-1). To use the
chat, simply type your comment into the message field on top of the chat window
and press the enter key or click on the "!" button.
Figure 3-1. the chat window
Special case options
When entering a new case or editing an existing case, there are some advanced otpions that can be configured. To change the case options open an case and click on the
edit icon in the toolbar.
Allow other users to add images
With this option, you can allow other users to add additional images to this case. This
might be useful if different analisys for one case are performed at different locations.
The results (with images) can be collected to one case.
Publish case
Published cases are visible and searchable by any user without the need of beeing a
member of your dicussion group.
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Chapter 3. Advanced Functions
Hide comments
Hidden comments can be used to prevent users from influencing each other. A user
can read the comments of others only after he has submitted his own comment.
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Chapter 4. Moderatoration of a Discussion Group
What is a moderator
Every group on iPath has at least one group moderator. Moderators are previlaged
users, who can control access to the discussion group. Additionally they are allowed
to change group options, that are needed to adjust the behaviour of iPath for different
applications.
Before going into details, we will quickly present some common uses of iPath and
how discussion groups may be set up to serve these uses. However, you are free in
using iPath for a different purpose. Most group pptions can be configured with the
"group settings" link located under the administation section on the main page (cf.
Figure 4-1).
Figure 4-1. the group settings dialog
Exmaple Configurations
General recommendations
Whatever purpose you want to use iPath for, consider one thing: every server in the
internet is potentially vulnerable to attacks by hackers. Therefore, if not absolutly
necessary, do not allow the members of your discussion group to store patient sensitive data. A simple method for preventing users from entering sensitive data like
name or birthday is to present a default desciption (cf. Figure 4-1), where you specify
what kind of clinical data should be given.
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Chapter 4. Moderatoration of a Discussion Group
Expert to expert consultation
For our first example we assume, that you are a group of specialist pathologists who
would like to discuss difficult cases on the internet. Figure 4-2 shows an example
setting for such a discussion group. As we assume that every member is a specialst,
we can allow everyone to add a final diagnosis to his own case. Additionally we can
allow users to change the names of their cases, as we can leave the responsibility to
know the real identity of a case to its sender.
Figure 4-2. possible group settings for second opinion consultations among experts
Many non-experts consulting a few specialists
This is the situation that is called "expert group" in iPath. A small number of experts
can be consulted by many other users. Typically, the core of experts can view and
comment all cases entered into the group, while common users can only see the cases
they have sent in. The configuration for this behaviour is shown in Figure 4-3. Don’t
forget to explicitly mark your expert users as experts under the group membership.
Figure 4-3. possible group settings for non-expert to expert consultations
Teaching: Setting up a group with a reference atlas
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Chapter 4. Moderatoration of a Discussion Group
Configuration of discussion group
Setting the group membership
Once the discussion group is configured, it is time to add group members. You can
either add new users to the iPath server yourself by clicking on the "add new user"
link on the administration section on the main page or by granting access to existing
users.
Grant access to an existing user
To grant access to one of your discussion groups to an existing user, simply select the
according user from the "user list" link (main page, administration). click on continue
or "gourp membership" on this page. On the floowing page (Figure 4-4) you can setup
the group membership for this user. The check at expert is only important when the
group is set up as an expert group (cf. Figure 4-3).
Figure 4-4. defining group membership
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Chapter 4. Moderatoration of a Discussion Group
24
Chapter 5. Administration of an iPath Server
well, this chapter will follow somewhen later.
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Chapter 5. Administration of an iPath Server
26
Bibliography
27
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