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Kevin Baensch 11 months ago
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[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

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