Cellcounter.jl

'Cellcounter' is a simple Julia package providing a GUI to manually count cells or cell features (e.g. outgrowths) from 2D images.

Installation

To use this package install Julia, next start a Julia terminal/REPL and use the following to add the package:

] add https://github.com/COMODO-research/Cellcounter.jl.git

Where the ] should trigger the package manager in your Julia REPL. Please note that Cellcounter depends on Makie, which is a very large project. Hence Cellcounter might take quick long to compile when it is first used.

Getting started

A basic use case if given in the examples folder which shows you can activate the GUI like this:

using Cellcounter # This activates the package functionality

# Define folder containing images
imageFolder = joinpath(cellcounterdir(), "assets", "example_image_data") # imageFolder ="mypath/myfolder"

cellcounter(imageFolder; numTypes=3) # Start the GUI

The last line there triggers the GUI for the image folder called imageFolder. Windows users may need to learn more about how to specify their path as a string. The optional input numTypes defines how many "things" or features are counted, e.g. use numTypes=3 if you are interested in counting 3 different things such as live cells, dead cells, and branches crossing the grid. Currently the GUI supports up to 9 types.

About the GUI

• Left click: Triggers a count increment for the current type when in "counting mode", or deletion of nearest when in "delete mode".
• Right click: Drag the image
• Scroll: Zoom in
• Delete key: Changes to "delete mode"
• Backspace key: Remove last added of current type
• Space bar: Return to "counting mode" from "delete mode"
• Number keys, e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9: Switch to counting this type
• Right arrow key: Go to next image
• Left arrow key: Go to previous image
• Bottom slider: Scroll between images
• Vertical sliders: The vertical slides control the strength of the red, green, and blue colors in the displayed image.
• Grid spacing: The grid spacing is adjusted by editing the text in this text box (top right). This should usually only be done once at the start of a counting session.
• Type menu: In addition to using the number keys, the type can also be switched using the type pull down menu.
• Save file name: To set the save file name, change the text in the long horizontal input box under the image. This should be a full path to a .csv file.
• Save button: This will export the counts to the set .csv file. Note that this action will always overwrite the file. So make sure you copy and rename the file manually if you do not wish to overwrite it.

Output

The output of the GUI is a .csv file for the entire image dataset contained in the folder provided. Below is an example for a counting results for 3 count types and 2 images.

Image,        Grid spacing, Type 1, Type 2, Type 3 
Image_01.tif,           45,     23,      8,      4 
Image_02.tif,           45,      7,      5,      9

Which when imported into a spreadsheet editer can be viewed as follows: