STARTING XID/MUDES

IF YOU ARE USING THE MUPCES DIRECTLY FROM THE CD:
 

•     Click on 2003Anatomy/XidW/XIDRO.EXE on the CD to start the program.

IF YOU ARE USING A SONY 505 LAPTOP ON WHICH THE MUPCES HAS BEEN INSTALLED:
 

• Double click the MUPCES shortcut icon.
•  When you open the XID program, the XID Database Selection Dialogue browse window appears which will show only XID Database files.  Select the C:2003anatomy/XidW folder on your Sony.
• Select the Plant Cell Types database  (PCELL.xid) Database file and double click it.
• If the program is not maximized on your screen, click the Maximize button in the upper right corner.
• The current screen shows "Menu Structure", "References" and "Database Description" in the upper left, a list of plant cell  names in the lower left window, and a blank window on the right.
• Right-click on the words "Menu Structure", click "Expand attribute menus.
• Click on the - box to the left of "Menu Structure" to contract the menu.

• Prepare your sections and/or macerations in advance, so you can concentrate on observing cell features and interacting with the MUPCES.
• Plan your histological staining work in advance, so the material is ready for observation when you need it.
• Closely examine the unknown cell  in its entirety, to form a good three dimensional image of what it looks like.
• Note any unusual features that are present.  Enter these first to reduce the database size and menu structure.
• Enter attributes that you are absolutely sure are present in your specimen.
• Utilize the Analysis feature to help you decide what features to look for next.

• Click the small + box to the left of "Menu Structure" in the upper left window. The first level of the menu structure expands.
• Click the small + box to the left of "Cytoplasmic Features" Submenu
• Double click One Nucleus. The number (12) to the left of the attribute (One Nucleus) is the number of cells in the database which display that characteristic. Note that the number of items shown on the line above the items list is now 12/19. This means that of the original 19 cells in this database only 12 meet the criteria selected. The remaining cells are shown in green and alphabetized at the top of the items list; the eliminated cells are shown in red and alphabetized below those remaining.
• Double click Inconspicous Vacuoles. Note that the number of items remaining is now 3.
• The next character which you will use is uniformly thin cell walls, which is not found under Cytoplasmic Features.
• Click the small + box to the left of "Cell Wall Features " Submenu.
• Click the small + box to the left of "Cell Wall Thickness " Submenu..
• Double click Uniformly Thin. Note that the number of items remaining is now 2.
• Click the small + box to the left of " Cell Geometry" Submenu..
• Click the small + box to the left of " Cell Shape in Transverse Section" Submenu..
• Double Click Isodiametric.  A message now appears on the screen: "Item Identified:" and provides you with a scrollable photo and description of the plant cell on the right. Click "OK" to clear the message.
• You can drag the split line (that divides the right and left portions of the screen) to the left if the entire image is not viewable.
• You can select what information is displayed for the species on the right side of the screen by clicking "Options", then "Species Description", and making your selections.
• Click the yellow brush icon in the tool bar along the left side of the screen to clear all marks in the tree. Note that the number of cells remaining returns to the original number in the key (19/19), and all of the menus and attributes return to a blue color.
• The right hand side of the screen now displays the highlighted species at the top of the species list. You can display the photo and description of any species in the species list by clicking on its name.

• If not already done, Click the small + box to the left of "Menu Structure" in the upper left window. The first level of the menu structure expands.
• If not already done,Click the small + box to the left of "Cytoplasmic Features" Submenu
• Right click One Nucleus.  Click Mark Yes in the drop down menu.  A YES mark now appears to the left of One Nucleus, and the number of items remaining is 12.  Note that a Double click is the same as setting a YES mark.  A "Y" mark now appears to the left of "One Nucleus", and the number of items remaining is reduced. You have said the number of nuclei in your plant cell IS one.
•  Click the Eraser icon (between "N" and "OR" on the left hand tool bar to clear the mark on the attribute. Alternatively, you can Right Click on the Attribute and then select Clear Mark. Note that the number of items returns to the original number (19/19).
• Marking more than one attribute in a menu with a Yes mark causes the attributes to be combined as "AND." For example: Double clickOne Nucleus. Note that the number of species remaining is 12. Double click Inconspicuous Vacuoles. The number of items remaining is now 3. You have said that your cell has BOTH a single nucleus AND inconspicuous vacuoles.
• Click the yellow brush icon in the tool bar along the left side of the screen to clear all marks in the tree. Note that the number of cells remaining returns to the original number in the key (19/19), and all of the menus and attributes return to a blue color.

• If not already done, Click the small + box to the left of "Menu Structure" in the upper left window. The first level of the menu structure expands.
• If not already done, Click the small + box to the left of "Cytoplasmic Features" Submenu
• Right click No Cytoplasm.  Click Mark No in the drop down menu.  A No mark now appears to the left of No Cytoplasm, and the number of items remaining is 12.  You have said that the No Cytoplasm feature IS NOT present in your cell, that is, your cell has cytoplasm. Note that the number to the left of "Green" still shows some remaining species. This is due to the fact that "NO" marks eliminate only those items that are marked exclusively for that character (in that menu).
• Click the yellow brush icon in the tool bar along the left side of the screen to clear all marks in the tree. Alternatively, you can Right Click on the Attribute and then select Clear Mark. Note that the number of cells remaining returns to the original number in the key (19/19), and all of the menus and attributes return to a blue color.
• To eliminate an item that can occur with more than one attribute in a menu, all possible attributes for that species must be marked as "NO" in the menu.  To understand this, try marking "green Chloroplast" NO.  Notice no cell types are eliminated.  This is because the abscence of chloroplasts by itself can not be used to eliminate any cell type from the data base.

• If not already done, Click the small + box to the left of "Menu Structure" in the upper left window. The first level of the menu structure expands.
• If not already done, Click the small + box to the left of "Cytoplasmic Features" Submenu
• Right Click Calcium Carbonate Crystals,Click Mark Or in the drop down menu. A dialogue box appears with the list of attributes in the menu with small boxes to the left of each.
• Click the box left of Protein Crystals or Aggregations.
• Click OK in the OR Window. The number of items remaining is now 2. You have said that you are unsure of the structures in the cytoplasm of your cell, but that they are either calcium carbonate OR protein crystals.
• Use the OR technique any time you are unsure of the exact answer. This is very helpful for features that are difficult to identify definitively without extensive analyses.
• Click the yellow brush icon in the tool bar along the left side of the screen to clear all marks in the tree. Alternatively, you can Right Click on the Attribute and then select Clear Mark. Note that the number of cells remaining returns to the original number in the key (19/19), and all of the menus and attributes return to a blue color.

•  Click the "A" button on the toolbar. A "List of Useful Menus" appears on the right.  This is a list of suggestions for attributes which will be useful in identifying your plant cell.  These attributes are listed in descending order for maximum convergence on identification of the unknown.  What this means is if you can use the first attribute, this has the highest probability of descriminating remaining items from one another.  Note, however, you can use these attributes in any order that is convenient for you.
• Click Cell Wall Thickness in the right hand window.  Notice that the Cell Wall Thickness submenu is now displayed and highlighted in the left hand window.
• Double click Uniformly Thin the Cell Wall Thickness submenu. Note that the number of items remaining is now 9 and that the Analysis Window has been reshuffled to give you new advice on what attibutes to examine.  Once you launch it the Analysis function works interactively to give you updated advice on the basis of your input into the system. The list of suggestions on the right should automatically reset to consider only the species not yet eliminated from the list. If it did not, click "Options" at the top of the screen, and click on "Auto Update", and then click the "A" button again. You can tell whether it automatically reset by whether the top suggestion has changed.
• Double click Cytoplasmic Features in the right hand window.  Notice that the Cytoplasmic Features submenu is now displayed and highlighted in the left hand window..
• Double click One Nucleus. The number of items remaining is now 7 and that the Analysis Window has been reshuffled to give you new advice on what attibutes to examine.  Once you launch it the Analysis function works interactively to give you updated advice on the basis of your input into the system..
• Double click Cell Shape in Radial Longitudinal Section in the right hand window.  Notice that the Cell Shape in Radial Longitudinal Section submenu is now displayed and highlighted in the left hand window...
• Double click Isodiametric The number of items remaining is now 4.
• Double click Parademal Section of Surface View in the right hand window.  Notice that the Parademal Section of Surface View submenu is now displayed and highlighted in the left hand window...
• Double click Isodiametric The number of items remaining is now 3.
• Double click Cell Wall Histology in the right hand window.  Notice that the Cell Wall Histology submenu is now displayed and highlighted in the left hand window...
• Click Lignin present and Mark No.  The number of items remaining is now 2.
• Click Suberin or Cutin present and Mark No.  The number of items remaining is now 2.

Click Wax Present and Mark No.  A message comes up that says "No analysis possible with only one species left" (this is due to the auto reset of the analysis function).
• Click "OK" to clear the message. A message appears: Item Identified and provides you with the name of the plant cell identified (Apical Meristem Cell). and the cell image comes up on the right.
• Click Reset XID to delete all marks you have made on the menus. Notice that the total number of  species remaining now returns to 19.

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• Expand the Menu Structure (by clicking the small plus (+) box to the left).
• Expand the Cell Wall Features menu (by clicking the small plus (+) box to the left).
• Expand the Cell Wall Histology menu (by clicking the small plus (+) box to the left).

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Click the small + box to the left of "Menu Structure" in the upper left window. The first level of the menu structure expands.

Click the small + box to the left of "Cytoplasmic Features" Submenu

Double click One Nucleus.

Double click Inconspicous Vacuoles.

Click the small + box to the left of "Cell Wall Features " Submenu.

Click the small + box to the left of "Cell Wall Thickness " Submenu..

Double click Uniformly Thin.

Click the small + box to the left of " Cell Geometry" Submenu..

Click the small + box to the left of " Cell Shape in Transverse Section" Submenu..

Double Click Isodiametric.  A message now appears on the screen: "Item Identified:" and provides you with a scrollable photo and description of the plant cell on the right. Click "OK" to clear the message.

 Click the check-mark icon on the tool bar. At the top of the window on the right it shows you what you have done, i.e., "Yes" for One Nucleus, "Yes" for Inconspicous Vacuoles, "Yes" for Uniformly Thin Cell Wall Thickness", Yes" for Isodiametric Cell Shape in Transverse Section".  No item will appear in the "Eliminated Items" section of this report unless you have eliminated them using the "Eliminate" command discussed later.

NB.  This command will be useful to you in completing your laboratory exercises in which you are asked to list the attibutes you used to identify different plant cell types.

• Click the small + box to the left of "Menu Structure" in the upper left window. The first level of the menu structure expands.
• Click the small + box to the left of "Cytoplasmic Features" Submenu
• Double Click No Cytoplasm
• Click "Database" at the top of the screen, and select "Common Attributes".  The attributes that are common to the remaining cells are listed in the right hand window.  What this tells you is that all cells without cytoplasm also have highly birefringent cell walls, thus birefringence of cell walls would NOT be a good character to use to try to identify your cells since all remaining cells have this feature.  In addition to giving you clues as to what features not to use in identification, Show Common Attributes can help you study the similarities among cell types.
• Clear all marks with the brush icon and then compress the Menu Structure.

• Click the blue "Item/Species List" icon on the toolbar to show a scrollable list of the species in the database along with a selection of information and images. Each time this button is clicked, a dialogue box appears asking what information you wish to have displayed (unless you have selected the box which says "Don't show this dialog before every report").
• The list displayed will be only those cells which have not been eliminated by attribute marking. Along with the species names, you may select to view a picture of the species, descriptive information, the filename of the picture in the database, and a list of references with page numbers where you may look up the species.

• Click the yellow Gallery button (overlapping squares) on the toolbar. Images of the species that have not been eliminated are presented, allowing you to scroll down through them. If the list of species is too long for all the images to be displayed, clicking on "More" at the bottom of the scrolled images will display the next group of images. You can change the size of the images, how many are presented (up to 100) and whether the species name is displayed with each image, by going to "Options", "Gallery" and making your selection. Since the images are of various sizes there may be some blank spaces in the gallery. You can also change the way that the gallery is presented by moving the "Split Line" that divides the right and left sides of the screen. If the names are included, the images are presented in a vertical arrangement. If names are not included, the images may also be presented in rows, depending on the width of the images and the width of the right window.
• Go to "Options", "Gallery" to select whether or not to show the names. Holding the cursor (not clicking) on any image for a couple of seconds will also cause its name to appear.
• Click once on an image to bring up the context menu.
• Click on "Find item in list" and the species list on the left will scroll down (if necessary) and highlight the species name.
• Click once on an image to bring up the context menu.
• Click on "Toggle eliminated", and a red X will be placed in front of the species name in the species list at the left, removing the species from those remaining. Since the species has been eliminated it is shown below those remaining in the list and its image is removed from the gallery.
• Click once on an image to bring up the context menu.
• Click on "Description", and the dialogue box for species description will appear unless "Don't show this dialog before every report" has been checked under "Options", "Species description" (in which case the selected information for that species will appear, replacing the gallery).
• Click the yellow Gallery button (overlapping squares) on the toolbar. Click once on an image to bring up the context menu.
• Clicking on "Distinctive attributes" will call up the distinctive attributes feature described in the section just below this.

• Right-click on the words "Menu Structure", click "Expand attribute menus.
• Double Click No Cytoplasm
• Right-click on Fibers  in the remaining items in the list in the lower left corner, and in the context menu select "Distinctive Attributes."
• A screen titled "Distinctive Attributes of" (name of items that was highlighted) appears. The number of cells with each attribute is listed on the left hand side of the screen in order of increasing frequency. Those attributes with a "1" at the left, are possible only for the cell named at the top of the screen. Attributes with a "2" at the left are possible for the cell named and for one additional cell from the items list, and so on. This screen should be thought of as containing features the cell MAY have. These features are not necessarily mandatory.  If your cell  had Slit Pits, however, this screen would have provided a good clue.
• Right-click on Phellem - Cork Cell  in the remaining items in the list in the lower left corner, and in the context menu select "Distinctive Attributes."  Here there are five attributes unique to Cork Cells that you could look for in identifying this cell type.
• Click the yellow paintbrush icon to clear all marks in the menus.
• Examine Distinctive Attributes of a number of cells in the items list.  Notice some cells have attibutes with a "1" at the left.  These can be considered "acid test" attributes, which if observed will allow you to identify the cell quite rapidly.  Other cells do not have attibutes with a "1" at the left, which means that a combination of attributes must be used to successfully identify these cells.
• Compress the Menu Structure tree, and click the yellow paintbrush icon to clear all marks in the menus.

• Click the small + box to the left of "Menu Structure" in the upper left window. The first level of the menu structure expands.
• Click the small + box to the left of "Cytoplasmic Features" Submenu
• Double Click No Cytoplasm
• Assume you know the specimen you are trying to identify is NOT a Vessel Element (because you're looking at a Gymnosperm).
• Highlight Vessel Element in the lower left hand window and click the blue "X" button on the tool bar to eliminate those species from consideration. This leaves an X mark to the left of Vessel Element, and moves it into the alphabetized list of eliminated cells below the those remaining. Eliminating cells in this manner can be very helpful. Now if you were to click "Analysis", the suggestions provided will be different than they would have been, since the program now tells you how to distinguish between only those that have NOT been eliminated.
• Click the check mark ("Marked & Eliminated") icon on the tool bar. This brings up a list of the attribute marks made, and below it the images of those cellss that have been marked as eliminated. Clicking on one of these images calls up a context menu that will find the cells name on the items list, toggle the cells back from being eliminated, or access descriptive information.
• Contract the Menu Structure tree and clear all marks using the brush icon.

• Expand the Menu Structure (by clicking the small plus (+) box to the left).
• Expand the Cell Wall Features menu (by clicking the small plus (+) box to the left).
• Expand the Cell Wall Histology menu (by clicking the small plus (+) box to the left).
• Right-click "Lignin Present", and select "Report".
• Advice with regard to what and how to look for the attribute is displayed in the upper right window.  A description and image of a plant cell with Lignified Cell Walls is displayed. If the entire screen is not visible you may use the scroll bars or drag the window divider to the left to enlarge the window.
• Right click on the menu title "Cell Wall Histology" and click "Report".  Here general advice is given with regard to how to proceed with assessing these attributes. With some menus an image appears that allows you to compare all of the different attributes. You can move the split line to the left or scroll the image if it is not all viewable.

• Right-click on any cell name in the list, then click "Description". If the dialog box allowing you to select the information you wish to have presented for that cell does not appear, it is because the "Don't show..." box is checked in "Options, "Item Description".
• This screen gives you general information about the cell which was highlighted. A picture of the cell may be displayed, as well as descriptive information, the name of the image file name for the species, the attribute data that has been entered in the database, and a list of references with page numbers for further information on the cell.
• Right-clicking on a cell name in the list can also allow you to eliminate the cell or show its distinctive attributes in comparison to the other remaining cells. This feature does not work for cells that have been eliminated by attribute marking or the "Eliminate" function.

• No matter where you are in the program, selecting "Help" from the program "Help" menu at the top of the screen, provides you with detailed help that explains how to use the XID software.
• Click the "X" button in the upper right corner to close the Program Help.

If you are sure your specimen has an attribute that is not in a menu (but the menu appears, with other attributes), your species might not be in the database, or the author may have chosen not to include that attribute. It is also possible that we may have made an error in the plant data. Each key includes thousands of data entries. If you believe you have found an error, please contact us, and we will correct the error and send you an updated key with our thanks.
In the database, "false" data is used when it will make the program more efficient for the unskilled user. For example, dandelion is marked both 5 (the correct answer) and > 10 (the way it looks) in the "Number of Petals" menu.
Many families have more than one name (i.e., Asteraceae and Compositae), and either one can be selected in the "Family" menu. To eliminate such a family, however, both names must be marked as "NO" in the "Family" menu.

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These keys to identify plants are comprised of a set of databases designed to run in the expert system software produced by XID Services, Inc. The databases are supplemented by color images of each species and line drawings to illustrate the terminology used within the menus. Such programs offer many advantages over traditional dichotomous keys. While originally produced to increase speed and ease of use, they also provide the ability to easily update the data and images, and are much cheaper to produce and more compact than hard copy guides. These databases include a large selection of plant characteristics from which to choose. In general, much more data are included on each plant than is necessary to identify it. With this abundance of data, the user can identify a plant using the characteristics most obvious and easy to describe. With each characteristic entered by the user, the program eliminates all species that do not have the combination of features entered.
BOTANICAL TERMINOLOGY:

The use of botanical terms has been kept to a minimum; however, some terms used to describe plants cannot easily be replaced by "common" words. Definitions of terms, and usually illustrations, are provided throughout the menus of characteristics. Terms are also cross referenced to an excellent illustrated glossary of terms, PLANT IDENTIFICATION TERMINOLOGY (Harris and Harris, 1994, ISBN# 0-9640221-5-X) which is abbreviated PIT.
SPECIES INFORMATION:
Information provided for each species may include synonyms, ethnobotanic uses and additional information to distinguish the plant from similar species and to separate varieties. Keep in mind that the data for each species is also available and constitutes an extensive botanical description.
HELP:
The instructions on the use of the XID software are all included in the Program Help. To access program instructions, select "Help" from the Help menu. Scrolling down through the text of Help information provides a detailed review of how to use the various features of the software.
ANALYSIS:
One of the most useful and powerful features of the program is the Analyze Feature. It provides a list of the easiest and most effective menus of characteristics to distinguish between the remaining species that have not yet been eliminated. In the Broadleaf database, the Analyze feature may be used at any time. However, in the database for Grasslike Plants, it is important not to use the Analyze feature until the plant family for the plant has been identified. In the Grasslike database, using the Analyze feature before the family is identified, runs a high risk of failing to identify the plant, because it may lead the user to an attribute menu for the wrong family. If the correct family is not known, one should first go to the Family Key menu; if the family is known, then go directly to the appropriate family menu and the program will identify the family after the first characteristic is entered.
INTERACTIVE IDENTIFICATION:
When using the program, SELECT SPECIMENS THAT ARE OF AVERAGE SIZE FOR THAT POPULATION. Many of the easiest characteristics for the untrained user will be found in the "General" menu. The user should first enter the most obvious or unusual one or two characteristics of the plant and then use the Analyze feature to get leads for where to go from there. If you are not sure whether a characteristic fits the plant to be identified, DO NOT mark it. If you are not sure which characteristic best fits the plant (a blunt vs. rounded leaf tip, for example), USE THE "OR" FEATURE to mark them both and ensure that the correct species will not be eliminated from consideration. Also use the "OR" feature for dimensions of leaves, etc. to avoid problems from specimens outside the usual size for that species. When using the Analyze feature, the user may select any of the menus listed, or select a different menu from the menu tree. Unless you have extensive training in plant terminology, avoid the more complicated or technical characteristics; they usually aren't needed anyway. Due to the large number of characteristics to choose from, there are literally hundreds of thousands of possible paths to identify the same plant. USE WHAT YOU KNOW, WHAT IS MOST OBVIOUS, AND MOST UNEQUIVOCAL.
PICTURES AND DESCRIPTIONS:
Once you have reduced the number of remaining species to a relatively small number, review the photos and/or descriptions using the "Gallery" or "Species List Report". It can take as many steps in the menus to reduce the number of remaining species from 12 to 1 as it does to reduce the number from 400 to 12!! These extra steps can greatly increase the possibility of making an error (especially since these species have greater similarities).
REFERENCES:
The "References" section (below "Menu Structure") allows you to see the ISBN # for the references used in the program, so that you can order those which you would like to add to your library. You can also "drag and drop" the references in the list so that those which you own will appear at the top.
This program is a tool to help in the identification of plants, and as with any key, should not be considered a final authority. Identifications should be checked against plant descriptions. A list of references and page numbers, describing the plant may be called up from the Species List.
We have made every possible effort to eliminate errors from the data. In the event you find data errors, we encourage you to Contact us, so we may correct them and send you a new copy. Also please feel free to contact us if you have a better image of any species that you would like to contribute. Photographic credits are included on any images used in the databases. The data and images are being continually updated for inclusion in future versions.
Please feel free to Contact us if you have any questions.

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How to Contact Us:
XID Services Inc.
PO Box 272
Pullman, WA 99163
800-USA-2-XID (800-872-2943)
rold@xidservices.com
rold@pullman.com
Our web site is located at www.xidservices.com
We may be contacted directly for technical assistance.
This program is produced using software created and produced by XID Services, Inc., Copyright 1992 - 2001.

If you wish to run this program on the hard drive of your computer instead of from the CD, create a new folder on your hard drive, and then (using Windows Explorer) copy all the files from the CD to the new folder. Once that is done you may create a new shortcut icon on your desktop to the executable which will open the program. Be sure there is at least 50 MB of free space on your hard drive. Also, if you have a copy of an older Windows version of XID software on your hard drive, there is a possibility your computer may default to running the program in the older version. If this happens, simply delete the older version.
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