[MIT License](./LICENSE)

# Colony Counter
A simple Utility to count and measure bright spots on dark images 😸

## Features
- Image transformation results are cached and incremental.
- Provides an ugly user interface with intuitive key binds.
- Batch process/export image analysis results.

- Adjust colony recognition and filtering through a couple of simple sliders.

![](./readme_img/Filter_Colony.gif)


- Remove false positives by clicking on them.

![](./readme_img/Remove_Colony.gif)

## Getting Started
- Install python (>=3.8 recommended... I made sure to explicitly use ordered dictionaries but just in case).
- Install dependencies in whichever way you prefer.
- Create the folders "in", "out" and "cache" (or run colonycounter.py).
- Adjust queue functions in source code to suit your needs (and read through [Caveats](#caveats)).
- Copy/Move your images into the "in" folder.
- Start the program by running the colonycounter.py file.

## Key Binds
| Key             | Function                                                                               |
|-----------------|----------------------------------------------------------------------------------------|
| q, left arrow   | load previous image                                                                    |
| w, right arrow  | load next image                                                                        |
| a               | apply changes (always do this before switching images, otherwise changes will be lost) |
| r               | reset changes that have not yet been applied                                           |
| l               | load saved settings from disk                                                          |
| s               | save currently applied settings to disk                                                |
| left mouse btn  | add colony to list of ignored colonies                                                 |
| right mouse btn | remove colonies in the vicinity from ignore list                                       |
| c               | clear list of ignored colonies                                                         |
| e               | batch process and export all images                                                    |

## Caveats
- The current processing queue expects 16bit gray scale images with the file extension .tif (tagged image file).
- watershed function does not work on 16 bit images... so there are some hard coded values to bring measurements back to 16bit brightness values
  - this means a loss of resolution
- To get hour and culture type values the following folder structure is expected:
  - "$DIRIN/OPTIONAL\_FOLDERS/$HOUR/$CULTURETYPE/image.tif"
  - $HOUR = integer followed by the letter h
  - $CULTURETYPE = whatever string identifies your culture type
- Code documentation is currently lacking
- Not all types are properly annotated