Microglia Counter — Study Notes

Function Definition in Python

A function definition begins with the keyword 'def', followed by the function name and parameters in parentheses, and includes a return statement.

int()

A Python function that converts a value to a whole number by dropping decimals.

float()

A Python function that converts a value to a decimal number.

str()

A Python function that converts a value to a string (text).

return False

Exits a function immediately and sends back the value False, skipping any code that follows.

Dictionary in Python

A collection that stores key:value pairs, allowing access to values by their corresponding keys.

min(255, max(0, value))

A function that clamps a value between 0 and 255 to keep pixel values valid.

For loop with two variables example

Unpacks tuples in a list, assigning the first and second elements to x and y, respectively.

try/except block

A construct that executes code that might fail, with a mechanism to handle errors elegantly.

Parameter vs Argument

A parameter is a variable in function definition; an argument is the actual value passed to the function.

dict(params)

Creates a shallow copy of a dictionary, allowing modifications without affecting the original.

append() method in Python lists

Adds an item to the end of a list.

Normalization

The process of rescaling pixel values to a range of 0 to 1 to ensure consistent image brightness.

Otsu thresholding

An algorithm to find the optimal cutoff value to separate foreground from background in images.

Solidity

A metric defined as cell area divided by bounding box area, indicating shape compactness.

Circularity

A measure calculated as 4π times area divided by perimeter squared, with 1.0 indicating a perfect circle.

F1 score

A harmonic mean of precision and recall used to assess the accuracy of binary classifications.

Grid search

A method of parameter tuning that tests all combinations of given parameter values.

Binary mask

An image where specific pixel values mark regions of interest, usually represented in black and white.

Abstraction in programming

The process of breaking down complex tasks into smaller, manageable functions.

Thread.sleep(2000)

Pauses execution for 2000 milliseconds to allow a window to fully open before proceeding.

XML

A structured text format used for storing and transporting data, known for human-readability and tool compatibility.

ImagePlus in Fiji

The main image object that holds pixel data, dimensions, and metadata within Fiji/ImageJ.

ImageProcessor

The object that manipulates pixel data within an ImagePlus, allowing mathematical operations.

IJ.run(imp, "Gaussian Blur…", "sigma=3")

Executes the Gaussian Blur command on an image with a specified blur radius.

ParticleAnalyzer

A Fiji tool that detects and measures connected regions in binary images.

RoiManager(False)

Creates a hidden ROI Manager in Fiji that does not appear in the UI, reducing clutter.

GenericDialog in Fiji

A class that creates pop-up input dialogs for user interaction within Fiji.

Overlay in Fiji

A layer for annotations on an image that does not change the underlying pixel values.

Jython

A version of Python that runs in the Java Virtual Machine, enabling Python code to interact with Java objects.

Iba1 and P2RY12 channels

Two microglia markers used together to decrease false positives by confirming detection with both.

DAPI usage

A dye that labels all cell nuclei, used to validate detected blobs by ensuring they contain actual nuclei.