代写A virtual laboratory on cell division代做Java程序
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Contents:
• Background and logic
• Assignment
• Instructions for using the excel files
• Instructions for using the 3D cell viewer
• Counting and analysis
Background and logic:
You will conduct an analysis of the stages of cell division using real data provided by the Allen Institute for Cell Science in Seattle, WA and freely available on their website https://www.allencell.org. Mitosis is adynamic process; however, you will analyze still images which will mimic the kind of data collection and analysis performed by both basic science
(https://bmcvetres.biomedcentral.com/articles/10.1186/s12917-017-1030-7) and commercial
(https://patents.google.com/patent/US20180095070A1/en) laboratories. The experimental logic can be thought of as follows:
Suppose you are interested in the behavior of an organism; let’s say zebras. You are interested in how much time they spend eating, sleeping, running, conducting “zebra” play and soon. You could make a movie of individual animals, but this might be very inefficient. Getting one zebra’s worth of data for one day would take you a whole day of filming. Instead, you could take random images of a herd of many
zebras and then count the zebras in each image doing specific things. This might be more efficient than filming one zebra at a time, but you’d have to think a bit about how to interpret the data. For one thing, if an event was very short (say only a minute or two), you might miss those events by taking random
pictures, unless you took a lot of images and looked at a lot of zebra pictures. Now imagine that to
gather more data you hire someone to take images for you, but when you analyze the images you
discover that there were no sleeping zebras in the images. You might conclude that zebras do not sleep, or that they sleep for very short periods of time. On the other hand, you might conclude that your
assistant was sleeping instead of taking pictures while the zebras were asleep. So, there are lot of things to consider when designing the experiment and interpreting the data.
Assignment:
There are two parts to this assignment.
Part 1: Create and discuss a hypothesis regarding what you expect to see. In part 2, you will be analyzing a number of images containing pictures of cells stained to reveal their DNA and mitotic spindles, and you will use your knowledge of the events of mitosis to count the cells at each stage: Interphase, Prophase, Prometaphase, Metaphase, Anaphase and Telophase. Do you think all stages will have equal counts?
Why or why not? If not, which stage of mitosis do you think will be most, least, etc. common in your
data and why? What do you know about what happens at each stage of cell division, and how long
(relatively) might that require? Note: most of the cells will be in interphase, because it is the longest part
of the cell cycle. The assignment is to discuss the stages of mitosis. Do not tell me your hypothesis is that most cells will be in interphase.
Send me your hypothesis discussion, and I will grade it and then provide you with material to complete part 2 (see part 2 for further details) including an Excel spreadsheet as well as examples of cells at each stage of the cell cycle from the data set as “training” .
Part one should require at most one written page and about 20 minutes of your time.
Part 2: After you turn in your hypothesis, you will get an Excel spreadsheet as well as examples of cells at each stage of the cell cycle from the data set as “training”. The first column in your Excel file will
contain links to fields of cells on the Allen Institute for Cell Science website. The links are labeled “Image 1”, “Image 2” and soon. Click on each link and animage should open in your default web browser. You will count all the cells having enough of the nucleus in the image to identify its stage, enter the numbers and then tabulate the results from several images (at least 20). See below for some suggestions on
counting if there are many cells in the image. You will then generate a graph, table orchart that shows your results. Finally, you will write a discussion that addresses whether or not the data support your
original hypothesis and why or why not you think that happened. You will also discuss the value of this exercise (or lack thereof) in assisting you with understanding mitosis specifically and the science of cell biology in general.
Part 2 should be possible in one or at most two written pages and should take less than 1 and a half hours of your time. Please let me know if you have any questions or any technical difficulties.
Instructions for using the Excel files:
You will receive an Excel spreadsheet that contains links to a web-based cell viewer hosted by the Allen Institute for Cell Science. Clicking on each link should open animage in your default web browser.
Once you have counted the cells at each stage for animage, enter the total number of cells at each stage of the cell cycle in the table in the row for that image. Include interphase as well as the other stages.
Instructions for using the 3D cell viewer:
The 3D Cell Viewer is a powerful web-based tool for accessing and visualizing cell data hosted at allencell.org. The viewer has many features and you are welcome to explore them at your leisure.
However, completion of the exercise will only require you to know how to use 4 parts of the viewer and what they do.
Overview of the Cell Viewer:
The panel on the left is used to access different image sets. You will NOT need it for this exercise.
The main view panel is where you will see the fields of cells for analysis. The Z slider allows you to change the focus of the virtual microscope and increase or decrease the depth of focus (the amount of each cell that is seen). I recommend increasing the depth of focus, as described below.
The right-hand panel controls how each field of cells appears. There are many options, but I recommend just using the Alpha-tubulin checkbox to show and hide microtubules. Some images may also look better if you adjust the brightness using the left-hand part of the brightness slider.
Following area series of steps that I suggest using to make the view of the cells easier to interpret.
The first thing I do is open the space between the limiting arrows to show a bit more of the cells. (Red circle)
It may also be helpful to grab the leftmost handle on the intensity slider and move it slightly to the right (green circle).
Like this …
It may be helpful to toggle viewing of the microtubules, using the alpha-tubulin checkbox
With microtubules shown, you can see this is a mitotic cell – but which stage?
Sometimes, you can page through the images with the “play arrow” (blue arrow) and get a better idea of what the cell looks like:
Most cells can be identified using the XY images that appear in the viewer by default. Occasionally, you may find a cell whose stage can’t be identified easily using the XY view. You can choose to ignore them, but you might want to give looking at the cell from the side a try. To do this, click on “XZ” at the top right of the screen, instead of “XY”. Then click on the play button to move through the layer of cells.
There is it on the right! This cell is in metaphase!
Counting and analysis
It is recommended that you look at the DNA staining and microtubules separately to begin analyzing
each image by checking and unchecking the appropriate checkboxes on the right-hand side of the 3D
Cell Viewer. This will help you rapidly identify mitotic cells, since their microtubules and DNA are
different than that of interphase cells. There are also relatively few cells undergoing cell division in each field, so they are easy to count. However, interphase cells are numerous. In some images you will
encounter only a few cells, and it will be easy to count all the interphase cells by just looking at the image. However, other images may have a lot of cells, and it can be hard to keep track of them all. Below are some solutions:
A low tech solution is to put a piece of transparent plastic over your computer screen and then use a marker to check off each interphase cell as you count it. Believe it or not, this used to be the main way that scientists counted things in digital images in the past.
Snipping tool for Windows. If you have a Windows PC, you can use the built in “Snipping Tool” application. See here (https://support.microsoft.com/en-us/help/4027213/windows-10-open-snipping- tool-and-take-a-screenshot) for instruction on how to access the snipping tool if you are not familiar with it. The tool is available for Windows 7 through the current version.
To use the snipping tool, start the application and then chose “New Snip” (Cntrl-N). Then draw a boxaround the image of the cells. Use the marking tools and options to set up a thick pen in a color that’s
easy to see. Click (mark) each cell as you count it and then write the total number of counted cells down in the appropriate column of your Excel file.
Preview for Macintosh Computers. On a Mac computer, you can do something similar using the screen shot commands and the built in Preview application. First, press Command-Shift-4. A cross-hair cursor will appear, and you can click and drag to select the area of your screen you wish to capture. The function will save animage on your desktop or other location that you designate. Double clicking on the imagefile will open it in Preview. You can make marks on the image to keep track of the cells you count using the pen tool, and you can change the thickness and color of the marks using the tool options shown by the green arrows in the image below.
ImageJ. Finally, if you are interested in using a real scientific image analysis program, consider downloading and installing the free opensource image analysis program maintained by the National Institute of Health called ImageJ (https://imagej.nih.gov/ij/). The program requires java to run, but it is a state-of-the-art scientific image analysis program available for both Windows and Macintosh computers with a wide variety of features and capabilities. You can find a discussion of how to use the “point tool” for marking and counting image features here (https://imagej.nih.gov/ij/docs/tools.html)