Funding

  Project Proposal:   
  SIMSCOPE: Applications of simulated microscopy and video editing for the
  development of multimedia teaching tools in biological sciences (First-year)

  Participants:
  UCR, UCD

  Principal Investigators:
  Paul De Ley, UCR

Multimedia teaching tools are rapidly becoming an essential component of higher education, and show great promise in the teaching of science courses dealing with microscopy or microscopic subjects. A TLtC mini-grant has allowed the construction of a prototype CD and website, combining Video Capture and Editing (VCE) with hypertext files to teach nematode biology and simulated microscopy to undergraduates. The development of these prototypes has generated great interest among a much wider range of faculty at UCR and UC Davis, who wish to expand on these first prototypes and develop similar tools for teaching other science subjects.

Our combined group of faculty has access to a great variety of instructional materials and teaches a wide range of courses in nematology, biology and parasitology, often with the aid of customized internet websites. All of us are faced with similar problems of teaching students how to use microscopes, and most of us are not yet equipped to obtain and edit video content. We therefore request assistance from TLtC to provide the resources to develop skills and new tools with VCE, as well as improved website tools. We propose to greatly intensify instructional synergy across two campuses and five departments, by applying these tools in a broad collaborative context focused on the production and exchange of VCE-based multimedia teaching tools for microscopy.

  Instructional problems:

a) Microscopy and teaching

The microscope is an essential tool in many science courses, but the large size of introductory classes typically precludes laboratory experience with access to sufficient numbers of microscopes. Even where available, student microscopes paradoxically provide the poorest level of resolution to those who arguably need it most: undergraduate students with no prior experience. Slides with the clearest specimens are usually reserved for demonstration, because they are short-lived in inexperienced hands. As a result, students obtain a poor first impression of practical microscopy, and many are falsely led to conclude that they lack the personal skills required.

Microscopy is also instructionally difficult for more subtle reasons. First, it requires students to become familiar with all the controls and parts of the microscope. Second, the development of actual observation skills can only begin after students have familiarized themselves thoroughly with operation of the microscope. Observation is actually more difficult than operation, as it relies on the intuitive reconstruction of three-dimensional mental images of the observed structures, and this skill can only be acquired through experience. Third, students can read notes outside class hours, but they cannot practice with a microscope, and no online environment exists to provide an appropriately similar context. Fourth, traditional microscopy demonstrations do not allow instructors to interact with more than one student at a time. These problems are compounded by biology labs typically having 15 or more students per section for a limited number of lab hours, leaving minimal time for extensive instructor-student interactions.

b) Introducing video into the teaching environment:

Before VCE technology can be used effectively in teaching, it is essential that the teachers themselves first learn how to use it. Compared to still image editors and webpage designers, most software needed for video editing is not significantly more difficult to learn. Nevertheless, most faculty have not yet developed video editing skills, because for most of us reasons to incorporate those into our research programs have not yet been recognized, and hence no extramural context for acquiring video editors and learning how to use them.

c) Acquiring and exchanging video content for teaching applications:

As with all IT resources, a multimedia teaching tool can only be effective if it has sufficient information contents, and if these are customized and organized to suit the course subject. While many of us teach a range of subjects and have access to a wide selection of texts and still images, it is as yet much harder to find enough video clips with the right subject matter. This is especially true for more specialized courses with limited enrollment, and it is a major limitation even for those among us who do already have video editing equipment and experience. Conversely, some faculty members are already applying VCE as part of their research and extension activities, but they do not themselves teach the courses that would benefit most from this material. They also rarely have the time and resources to edit and adapt their video material to suit the needs of other faculty who do not yet have their own video capabilities.

  Previous results:

De Ley and Baldwin have developed a first very limited prototype of a VCE CD-ROM* as a handout for NEM/XRC205 "Identification of Plant Parasitic Nematodes", taught last summer at UCR. Participants were on average already experienced in microscopy, but included some beginners, and all were very enthusiastic about the CD. With the support of a TLtC mini-grant, De Ley, Baldwin and Nadler have then developed a CD-ROM with greatly expanded contents and functionality, and introduced this as a study aid into NEM/BIOL159 "Biology of Nematodes", taught during spring quarter 2002 at UCR. This CD addresses mainly instructional problem (a) above (teaching microscopy), more specifically the problems of allowing students to acquire observational skills, and of improving knowledge transfer from instructor to student (see appendix A). It specifically utilizes the ability of video clips to capture the action of focusing through a semitransparent microscopy specimen, and to mimic this focusing action during playback by allowing the viewer to move backwards or forwards through each clip.

  Proposed innovations:

We propose to collaborate intensively to introduce multimedia teaching tools for microscopy subjects in a wide range of courses at UCDavis and UCR. More specifically, we request funding to acquire software and training for video editing and multimedia integration applications, to allow for travel and meetings facilitating production, exchange and post-production of video contents, to support student helpers who will assist with the basic aspects of VCE, and to support the cost of post-production services by multimedia specialists at UC Davis and UCR. Hard copies of the created teaching tools will be distributed on CD rather than on DVD, because DVD hardware is not yet sufficiently widely distributed to ensure that all students will be able to access DVD copies in 2003.

Our long-term objectives are to disseminate video editing skills and facilitate development of microscopy-based teaching tools across all UC campuses for as wide a range of courses as possible. To maintain focus and manageability for 2002-2003, we will limit our efforts specifically to the following major themes:

a) Development of the front end and optical algorithms for virtual microscopy:
The prototype CD produced with support of the TLtC mini-grant only mimics the focusing and observation aspects of microscopy. In order to improve the speed and quality of student training in microscope operation, we propose to develop an interactive image of a microscope that will simulate all the basic controls and operations of a student microscope. This "virtual student microscope" will be made available to lower-division undergraduate students on a CD and via a dedicated website.

Dr. Cardullo and Dr. Carter both have access to advanced microscopy equipment, including confocal systems. Dr. Cardullo has already developed a set of advanced microscopy exercises, in the context of his annual Analytical and Quantitative Light Microscopy course at the Marine Biological Laboratories in Woods Hole. Dr. Carter has experience in developing optical performance calculators for confocal microscopy. Their expertise and resources will be combined with those of IET Mediaworks to develop a CD with customized exercises and simulation modules for interference contrast and confocal microscopy, aimed at upper-division undergraduates.

It should be noted that several "virtual microscopes" have been produced for other reasons (e.g. http://met.open.ac.uk/vms/vms.html, http://micro.magnet.fsu.edu/primer/virtual/virtual.html, http://www.cs.umd.edu/projects/hpsl/ResearchAreas/vm.htm). Although several of these sites are excellent resources, they are restricted in various ways, for example simulated operations are not operated via an interactive front end, the range of simulations is limited to certain techniques only, full access is only possible at a significant charge, etc. Most importantly, none of these sites is aimed at training undergraduates in the use of a basic light microscope by means of an interactive image that actually represents a generic microscope.

To be implemented by: Dr. Richard Cardullo (Biology, UCR), Dr. David Carter (Botany & Plant Sciences, UCR), Dr. Paul De Ley (Nematology, UCR), Dr. Harry Matthews (IET Mediaworks, UCDavis), Dr. Becky Westerdahl (Nematology, UCDavis)
Virtual student microscope to be used in: BIOL005B Introduction to Organismal Biology (approximate annual enrollment or AAE 145), ABI50B Animal Biology (UCDavis, AAE 30), BIS10V Virtual General Biology (UCDavis, AAE 150).
Advanced microscopy exercises CD to be used in the following courses at UCR: BIOL109 Laboratory in Cell and Molecular Biology (organized in alternate years, approximate enrollment 15), BIOL113 Advanced Cell Biology: Membranes, Organelles, and the Cytoskeleton (AAE 30), BIOL114 Advanced Cell Biology: Cellular Reproduction and Signaling (AAE 30), BPSC135 Plant Cell Biology (AAE 20), BPSC/BIOL138 Morphology of Vascular Plants (AAE 25).

b) Creation of a "Virtual Arabidopsis" CD and website:
Arabidopsis thaliana is an essential model for a wide range of genetic, physiological and mutational studies in plants, and directly relevant to a wide range of botanical courses. We propose to develop a multimedia teaching tool that would represent the wild type plant as well as selected mutants, to show how the mutant phenotypes differ. An image map of each "virtual weed" would provide links to a gallery of images and video clips of pollen, flowers, seeds, leaves, roots etc. at different magnifications.

To be implemented by: Dr. David Carter, Dr. Natasha Raikhel, Dr. Zhenbiao Yang (all Botany & Plant Sciences, UCR).
To be used in the following courses at UCR: BPSC/BIOL104 Foundations of Plant Biology (AAE 80-100), BPSC/BIOL132 Plant Anatomy (AAE 10), BPSC135 Plant Cell Biology (AAE 20), BPSC/BIOL138 Morphology of Vascular Plants (AAE 25).

c) Creation of a "Virtual Lab for Cell Biology and Neuroscience" CD and presentation:
The equipment/software requested in this proposal would be used to digitize images of histological microscopy sections and to create movies to complement the lab exercises for NRSC169. Students would receive a disk at the beginning of the quarter, allowing them to study these data before and after class, rather than being able to view these data only during the labs and review sessions. The CD would also contain quizzes for each lab section, which would be used to keep them up to date with material and to allow them to check their understanding of each segment of the course as it unfolds. In addition, the CD would include video material on human development. One of the most important aspects of teaching developmental anatomy is being able to show students information in three dimensions, the best solution for which are 3D movies. Dr. Talbot already has a number of videos that could be included, and others will be made or created with the requested equipment. The CD will also serve a valuable purpose as a resource that the students can use at any time in the future when they need to consult or review the information in the course.

To be implemented by: Dr. Prudence Talbot (Cell biology and Neuroscience, UCR)
To be used in the following course at UCR: NRSC169 Human Embryology (AAE 55)

d) Creation of multimedia teaching tools for courses in Nematology, Parasitology and General Biology:
Because of the many parallels in subject matter between courses taught by faculty of the nematology departments at UCR and UCDavis, all collaborators from both faculties will produce, exchange and adapt video contents to maximal advantage. The planned interactions and targeted courses are summarized in the table in Appendix B. In brief, we intend to produce teaching tools for a total of 17 courses, including 15 CD's with virtual slides and/or virtual labs, 11 websites for courses taught partially or fully online, and Microsoft Powerpoint presentations with embedded video for 4 courses.

Some collaborators will have more specific roles in the exchange process. Microscopes in the laboratories of Dr. De Ley, Dr. Baldwin and Dr. Nadler will be available as general facilities for obtaining VCE microscopy clips, to be used by those collaborators who do not have all the equipment required in their own laboratory. Dr. Baldwin and Dr. Nadler are curators of two of the world's largest collections of preserved nematodes and will continue to produce "virtual specimens" of important nematode species. Dr. Becker and Dr. Ploeg (UC Organized Research and Extension appointments) have no teaching appointments, but both are willing to provide video contents pertaining to plant nematodes and their control. Dr Ploeg and Dr. Westerdahl already have a range of edited and unedited video clips, which will be made available to the relevant collaborators for post-production and integration into course materials. Dr. Becker, Dr. Westerdahl, Dr. Caswell-Chen and Dr. Roberts are conducting or will conduct research in the quarantine facilities of the respective departments, and will provide video microscopy clips using VCE equipment provided by matching funds from the respective campuses (see below).

  Other activities:

a) Training of faculty and student helpers:

In order to successfully develop the tools listed above, we will initially organize a two-day joint training session in September 2002 for all faculty and student helpers involved, to be held at the Digital Production Lab (UCR) with joint presenters from IET Mediaworks (UCDavis) and Computing & Communications (UCR). Participants will be instructed in the use of video editing software (Premiere, Final Cut Pro) and web authoring software (Flash, Dreamweaver).

b) Planning and exchange meetings:

Following immediately on the training sessions at UCR for training, all participating faculty will meet to summarize availability of existing video material, to compare mutual needs for new material, and to finalize production plans accordingly. A second two-day joint meeting will be held in March 2003, to demonstrate prototypes and final versions of the created tools, to review availability of and demand for additional video material, to visit IET Mediaworks in order to finalize post-production of more complex material, and to coordinate completion efforts on those tools that still require it.

c) Virtual access to quarantine facilities and organisms:

UCR's Department of Nematology currently has a functioning Nematode Quarantine Facility, and UCDavis is in the process of constructing a new Contained Research Facility. Both of these are or will be the setting for research on invasive organisms that are highly destructive to agricultural crops and are therefore of immediate relevance to Nematology and Parasitology courses. Because of the strict regulations on access to and removal of material from these facilities, it is at present not possible to incorporate live recordings of the behavior of quarantine species, nor is it practical to illustrate quarantine methodology in its actual settings. We propose to equip both facilities with VCE equipment that will be used to produce video clips and still images, which can then be sent out via ethernet with no risk of accidental release of the quarantine organisms. This equipment will be financed with matching funds provided by UCR and UCDavis.

d) File storage and exchange:

Password-protected server space will be made available at no cost by Computing & Communications (UCR), to allow efficient file exchange between collaborators by FTP.

  Future plans:

If awarded, the one-year Full-implementation Grant will not only provide us with the means to create the products and skills listed above, but it will also allow us to prepare for further expansion of our efforts. Specifically, we intend to seek extramural funds from potential sources such as FIPSE, USAID Institutional Partnerships Program, ECA Internet Access and Training Program, etc. We also intend to request a second year of Full-implementation Grant funding from TLtC, with the specific purposes of:

• Extending our collaboration to other departments and UC campuses
• Integrating the "virtual student microscope" front end with the advanced microscopy simulation tools, to produce a "virtual differential interference contrast microscope" and a "virtual confocal microscope"
• Updating and expansion of all tools created for CD distribution in 2002-2003, and conversion to DVD format (we expect DVD technology to be readily accessible to all students by 2004 or 2005). This will apply for all relevant courses, and will require a training component in the use of DVD authoring software.

  Specific Aims

The aims of our current planning project are:

(1) To produce a CD and website for use in the following courses: NEM/BIOL159 Biology of Nematodes (UCR), NEM/XRC205 Identification of Plant Parasitic Nematodes (UCR) and NEM 110 Introduction to Nematology (UCDavis). We aimed to include 20 specimens from at least 10 species on the CD, and another 20 specimens from at least 10 species in the website.

As originally planned, all specimens to be included would be from preserved material kept in the nematode collections at UCR and UCDavis. However, during demonstrations of live material in the initial two labs for NEM/BIOL159 it became abundantly clear that the students would benefit from having video clips of live nematodes (especially behavioral and size mutants) and other microscopic organisms. We therefore adjusted our aims and deferred some of the editing of preserved material, in order to include more video clips of live organisms.

We are currently improving on the beta version of our CD on the basis of evaluations by the students of NEM/BIOL159 (see below), by adding further hyperlinks to the various files, and in order to adapt the contents to meet the slightly different emphases given in NEM110 at UCDavis. This improved version will also be integrated with the online teaching tools for NEM/BIOL159 already implemented in UCR's Blackboard system by Dr. Leo Schouest and collaborators.

Due to previously unforeseen scheduling conflicts, NEM/XRC205 will not be organized in the summer of 2002, but will be resumed in the summer of 2003. For this year, we have instead used the NEM/BIOL159 CD in two different ways to reach audiences similar to the potential students for NEM/XRC205: we have demonstrated the CD during the 34th California Nematology Workshop (De Ley, March 26-28, see below), and we have incorporated it in the teaching of a three-day training course at Mira Costa College, Oceanside (Baldwin, April 9-11, 2002).

(2) To develop plans for extensive collaboration involving many more collaborators and biological disciplines. As outlined in our application, and discussed in more detail below, we have been successful in generating widespread interest in VCE-derived teaching tools for microscopy-related courses.

  Planning Outcomes

Creation of a microscopy CD for NEM/BIOL159:

We constructed a beta version of a "virtual microscopy lab" on CD for the students of NEM/BIOL159 (four copies are submitted to the UCR TLtC office along with this application). The CD in question contains 7 complete virtual nematode specimens belonging to 6 different species, as well as video recordings of eight different mutants of the genetic model organism Caenorhabditis elegans, and video recordings of three other examples of microscopic soil invertebrates. The video clips are integrated with different sets of web pages, respectively containing diagrams of nematode anatomy (adapted from the diagrams used in the classes), and image maps providing an overview of a complete nematode. Other web pages provide a glossary of technical terms, and a brief description of the purpose of the CD: teaching students how to use focus as an integral part of the act of observation through the microscope.

Completion of the CD took longer than expected, especially in terms of constructing image maps and embedding these in hypertext pages, to link them to each other as well as to the video files. These last steps in the process were mainly implemented with the HTML editing features in Microsoft Word and in Netscape Composer, which are clearly not very efficient tools for the purposes of embedding image maps and video clips.

Introduction of the NEM/BIOL159 CD to the students:

The CD was completed just in time for inclusion in the last class of NEM/BIOL159. 30 upper-division undergraduate students were provided with a copy of the CD, and given a demonstration of how to access its text, image and video files using an internet browser like Internet Explorer and Netscape Communicator. The students were clearly interested in the demonstration, and surprised by the use of video clips as simulations of focusing action. They were also given a short questionnaire on the accessibility and usefulness of the CD. Results of the 7 returned and forms were as follows:

1. Do you think this CD is useful for understanding and studying this course?

Not at all: 0 Not very: 0 Somewhat: 3 Very: 4

2. Did you experience technical problems accessing the files?

No: 5 Yes: 2
(one additional student reported that she could not access the files at all and therefore did not return the questionnaire)

3. Did you find text errors or broken links?

No: 6 Yes: 1

4. Is the information logically presented and structured?

Not at all: 0 Not very: 0 Somewhat: 1 Very: 6

5. Feel free to give us any other comments or suggestions!

Only two responses:

"This would have been very useful at the beginning of the course. This CD was very helpful in showing what the nematode structures look like. Good job!"

"...(detailed description of a technical problem accessing the video files, and short list of more information from the course that should be included, followed by:)..Overall, it should be a very helpful tool in viewing nematodes & seeing structures that are hard to see in the lab!"

In terms of number of responses, we conclude that enthusiasm among students was not exceptionally high or low, as could be expected from the late introduction of the CD into the class. We did not insist that all students return the questionnaire "or else...", as this would have compromised the sincerity of their responses. Most students of the responding did not experience significant technical problems, but accessibility can clearly still be improved, and the minimum hard- and software requirements need to be stipulated more clearly.

Meeting at UCR:

Dr. Steve Nadler and staff member Ashleigh Smythe visited UCR for three days (March 6-8) to bring selected material and use it for a hands-on workshop on video capture and editing, using the system in the De Ley lab. We also commenced the planning process for the full implementation grant. The following was our agenda for the workshop:

Wednesday March 6th

* noon - Arrival at Ontario Airport, lunch.
* afternoon - hands-on of the various steps of capture and basic editing from slides and live material using both FinalCut on Macintosh and Premiere on a PC platform.

Thursday March 7th

* morning - advanced editing: adding titles, scale bars, arrows and labels to clips.
* noon - lunch
* 1.30-3.30 pm - Brainstorming session with Dr. Leo Schouest of Computing & Communications.
* remainder of the afternoon - construction of image maps to link all clips

Friday March 8th

* morning - continued construction of image maps to link all clips
* noon - lunch
* afternoon - construction of the web pages that organize access to the clips, integration of draft webpages and sets of clips.
* 5 pm - departure

The agenda was adhered to on March 6 and 7, but on March 8th it became again obvious that the final steps of web page construction and integration require more efficient web design software. The brainstorming session with Dr. Schouest was extremely productive, e.g. in defining the virtual student microscope front end as an objective for the implementation grant, and in identifying better software solutions for the web design and page integration steps.

Meeting at UC Davis:

Dr. James Baldwin and Dr. Paul De Ley visited UC Davis with staff members Dr. Irma T. De Ley and Dr. Manuel Mundo for three days (March 26-28) to recruit collaborators, to settle on the main themes of the full implementation grant, to explore opportunities at the DANR nematology workshop for developing video-based nematode identification teaching tools, and to present the NEM/BIOL159 CD to a mixed audience of students, faculty and farm advisors at the 34th California Nematology Workshop. Our agenda was as follows:

Tuesday March 26th

* noon - arrival at Sacramento airport, lunch
* afternoon - meeting in Dr. Nadler's office, followed by DANR Nematology workgroup meeting (explore opportunities/needs for lesion nematode identification tools)

Wednesday March 27th

* morning - 34th California Nematology Workshop (talk to potential collaborators)
* noon - lunch
* afternoon - 34th California Nematology Workshop (demonstration of NEM/BIOL159 CD)

Thursday March 28th

* morning - planning meeting in Dr. Nadler's office (8.30-9.30 am), meetings with Dr. Caswell and Dr. Ferris (9.30-10.30 am), visit to IET Mediaworks and brainstorming session with Dr. Harry Matthews and collaborators (10.45 am - noon)
* noon - lunch
* 2 pm - departure

No commitment for support could be obtained through DANR (Department of Agricultural and Natural Resources) for identification tools for lesion nematodes species, because some of the workgroup members questioned the difficulty of identifying those nematodes. In other respects, this meeting was very helpful in raising interest among potential collaborators from both UCDavis and UCR. The brainstorming session at IET Mediaworks allowed us to identify and integrate the relevance of their expertise and services, especially with regards to post-production of video files, and the creation of an interactive front end of a virtual student microscope.

  Significance

Although we are still improving on the teaching tools produced with the support of the TLtC planning project, we already consider it to have been instrumental and highly successful, in enabling us to demonstrate some of the many potential applications of VCE microscopy. This has allowed us to bring together a large number of collaborators for a full implementation project. It has also highlighted that it is not sufficient to generate skills and tools for video editing, but that we also need to improve our software capabilities and knowledge with respect to web design.

Faculty on both campuses are greatly interested in possibilities for incorporating video material into their teaching of microscopy-related courses. This integration will be highly beneficial to students in a range of situations, such as theoretical courses without labs, courses relating to expensive equipment and advanced techniques that cannot be incorporated into truly hands-on labs, or labs that would otherwise require a 1:1 instructor/student ratio for maximal transfer of knowledge.

However, there is at present a definite barrier for UC faculty to learn how to use video software and hardware, both in terms of its limited relevance to research projects and funding, and in terms of allowing faculty members to acquire the necessary level of (basic) video editing and (more advanced) web design skills. We therefore consider it essential that our full implementation proposal not only focuses on the production of teaching tools for the students, but also emphasizes training and software availability for the instructors.

* The contents of this CD are accessible at http://faculty.ucr.edu/~pdeley/vCenema1/home.html