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I am currently doing research at a university and wanted to create custom code that would be able to analyze hours worth of images of neurons and determine if the neurons are on or off. I want to write the code myself and was just wondering where I can get started. For example, what kinds of things can I import into python to read light in tiff files and what kind of things do I need to import to extract that data into a table or graph?

Some clarification: The neurons are always in the same place in all the images. It is a black and white image. The images are hours worth of neuron activity, where an image is taken every second or so. I do not want someone to write the whole code for me, but for people to please tell me what kind of things are necessary to read light in tiff files and export that data into some sort of table or graph.

Thank you!

I am not allowed to show a photo as an example, but I am allowed to describe what it looks like. The background is all black. There are white dots on the images scattered all around. Some are neurons and I am able to locate where they are. In all of the photos, the location of the neurons are the same and some of the neurons are lit up and others are dark. Which neurons are lit and which are dark change from photo to photo.

I do not have any code done yet, as I am here seeking for a place to start in this project.

The expected output of the code looking at the neurons and seeing which ones are lit up is data in the form of a table, graph, or even a text file if a table or graph is impossible. The table would include either a 1 or 0, 1 indicating that the neuron is lit up, and 0, indicating the neuron is dark. For the graph, it would have a number representing a neuron (1, 2, 3 4, ...) on the y-axis and on the x-axis would be a 1 or 0. Each column would be one image and you would see how the activity of each neuron would change over time. I am open to any other form of data.

Conner T
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You can read your file as an image and convert it to a black and white image. then if you can specify which pixels are located at each neurons in image you can check pixel's values to check if the neuron is on or off. any way I suggest to search in image processing packages of python the solution for your problem is easy to find. and in the case you can not specify which pixels are located at each neurons in image maybe search in "image processing dilation and erosion" would help.

Good luck!

Somayyeh Ataei
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  • Thank you for your response! Do you know what package can read a file as an image and convert it back to an image? – Conner T May 25 '19 at 14:41
  • look at this question:https://stackoverflow.com/questions/7569553/working-with-tiffs-import-export-in-python-using-numpy – Somayyeh Ataei May 25 '19 at 19:27