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Posted: May 15th, 2022
Image J Lab 1 Assignment
As we have discussed in lab, science is on the cutting edge of new information and many times scientists have to describe/interpret/evaluate something that has not been defined before. The purpose of this laboratory is to evaluate histological images of the brain taken at very high magnifications and describe what you see.
It is alright to be unsure, it is alright to not know where to start. Many times, scientist follow a line of study only to find that after gathering information, a new line of inquiry is needed based on the current findings. Sometimes it is hard to know where to start evaluating. Don’t be afraid to try something only to find that it doesn’t seem to change between groups - start by trying counting, calculating, or measuring something. That initial measure may lead you to see something else in the image. Don’t be afraid to try different things and look at the images in different ways. Use the FIJI program to help you assess the images.
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Analyze the CM data set . You can select any set of images you would like to analyze. In each set there are equal numbers of “control” and “experimental” images. You will compare these two groups to one another to see if the experimental manipulation changed anything anatomically in the brain tissue in these images. Both the FIJI and SPSS software programs have to be used for submitted analyses. Both programs are available on the lab computers.
FIJI is available for free download at: https://imagej.net/software/fiji/downloadsLinks to an external site.
For the write-up:
1. Paragraph 1 – a detailed description of the structures in your images.
Look at the details of the images in your chosen folder. Describe what you see in the images in as much detail as you can. Even if you do not know what exactly you are describing, spend time defining and explaining the structures/formations you see in your images. You can include information such as:
- What was the first things you noticed about the images.
- did any patterns or details jump out at you right away?
- were there any obvious differences between the two groups?
This paragraph should include a detailed description of what you see in the images. You can include diagrams, sketches, or annotated portions of the image to help your descriptions.
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2. Paragraph 2 (methods) – a methodological description of the choices you made when deciding what factors to measure with FIJI.
Describe how your first impressions lead to the decision of what you were going to measure in your images. Explain the different measure you decided to try using the FIJI software. For this paragraph include a description of:
- the different measures you tried with FIJI --- cell area and cell count
- which measures worked well and why
- which measures did not work well and why
- information on whether certain measure led to a decision to try something else/evaluate a different aspect of the image.
3. Paragraph 3 (results) – a reporting of the statistical findings of at least 2 of the measures described in paragraph 2. The statistics should be reported using the statistical nomenclature provided in last week’s lecture: Indicate the statistic used, the statistical result, and whether the findings were significant.
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4. Paragraph 4 (interpretation/conclusion) – for the last paragraph, use the results to support your explanation of what you think is happening in your image datasets. You do not have any background information about the images, so you can only use what you know in general about cells/neurons/the nervous system to describe the changes you see in your images. Don’t be afraid to use your descriptions of the images to guide your answers. Explain what you think is happening in your dataset including potentially what the experimental manipulation may be. Your interpretation is your own – use the described changes you included in paragraph 2 to support your conclusion.
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