web based tools developed to help students understand cell ultra-structure

CELS191 - Cell and Molecular Biology

Web based tools developed to help students understand cell ultra-structure

Frog cell at Anaphase

Lisa Russell, Jo Forrester and Phil BishopDepartment of ZoologyUniversity of Otago

CELS191 - Cell and Molecular Biology

Cell ultra-structure Develop the students capacity to infer function of

different cell types based on their recognition of constituent organelles.

Images Katrin Geist and Richard Easingwood

CELS191 - Cell and Molecular Biology

Challenges facing large, first year biology classes:

Evident that students struggle to make the link between:

3-d structure of organs, tissues and cellular components from lectures

2-d images that they obtain from light and electron micrographs

CELS191 - Cell and Molecular Biology

Textbook examples of stylised ‘typical’ cells often represent an oversimplification of real life images students will view during the course.

Challenges facing large, first year biology classes:

CELS191 - Cell and Molecular Biology

Only a very limited time and resources to provide students with hands-on practical experience with microscopy

limited to light microscopy

Viewing electron micrographs (TEM and SEM) restricted:

Challenges facing large, first year biology classes:

paper exercises or as web-based activities

free online software available has limitations (Image J and Zoomify)

CELS191 - Cell and Molecular Biology

Image J Open source program Wide range of tools,

including a calibration toolLimitations: not user friendly requires detailed step by

step instructions to calibrate image, annotate image etc.

students must download program

x=1.40, y=0.627, angle=-131.56, length = 5.30

CELS191 - Cell and Molecular Biology

Zoomify freeware package high resolution imaging

Limitations of package: unable to calibrate or

calculate scale unable to add annotations or

a key

CELS191 - Cell and Molecular Biology

Project Develop a web-based tool to complement guided

learning exercises that investigate: how cell ultra-structure is imaged (microscopy

and scale) structure and function of common organelles cell diversity and ultra-structural differences

(simple versus specialised cells)

CELS191 - Cell and Molecular Biology

Project

Funded by a CALT (Committee for the Advancement of Learning and Teaching) e-learning grant

Collaborative project: Educational Media, Higher Education

Development Centre (Peter Vlugter and Ayelet Cohen)

Otago Centre for Electron Microscopy (OCEM) in particular Mr Richard Easingwood and Miss Katrin Geist

CELS191 - Cell and Molecular Biology

Project o Development of a range of high resolution EM images from a

range of cell types: ‘simple cells’ (plant and animal cells) and specialised cells (secretory and absorptive)

CELS191 - Cell and Molecular Biology

Ideal features of an image viewer:

Zoom and panning tool Annotation tool Interactive key Measuring tool (linear and relative area)

CELS191 - Cell and Molecular Biology

Zoom and panning tool

CELS191 - Cell and Molecular Biology

Annotation tool

NucleusDark stained areas – heterochromatinlight areas - euchromatin

CELS191 - Cell and Molecular Biology

Interactive key

CELS191 - Cell and Molecular Biology

Linear measuring tool

CELS191 - Cell and Molecular Biology

Measuring area

CELS191 - Cell and Molecular Biology

Grid tool

CELS191 - Cell and Molecular Biology

Application of the image viewer: Image viewer is now used in three first year courses

Biology 112 (Introduction to animal biology) Utilized in a practical laboratory Proportion of red muscle present within a cross section of

eel tissue subjected to differing hormonal treatments

CELS191 - Cell and Molecular Biology

Image viewer is now freely available throughout the university as a plug-in to UniTube (file sharing system, wide range of file types including images, videos and audio files).

Once uploaded the UniTube URL can be shared or embed it into Blackboard or any other website.

CELS191 - Cell and Molecular Biology

‘Build a cell’ game Online interactive game designed to test students

ability to link cell structure with function.

CELS191 - Cell and Molecular Biology

‘Build a cell’ game Four levels - in each level they have to essentially

build the specified cell from a range of cell components.o simple plant and animal cell, specialised

secretory and absorptive cells.

CELS191 - Cell and Molecular Biology

To progress through each level:o correct cell components in roughly the correct

frequency (1, 2-10 or extensive)o 3 attempts at each level, if incorrect they have

to start the game again.

‘Build a cell’ game

CELS191 - Cell and Molecular Biology

Ongoing developmentsImage viewer Develop the annotation tool further

o allow students to annotate and save images for reviewing

o potential for assessment

Build a cell game developing specific feedback