52 lines
2.8 KiB
Markdown
52 lines
2.8 KiB
Markdown
[MIT License](./LICENSE)
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# Colony Counter
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A simple Utility to count and measure bright spots on dark images 😸
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## Features
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- Image transformation results are cached and incremental.
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- Provides an ugly user interface with intuitive key binds.
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- Batch process/export image analysis results.
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- Adjust colony recognition and filtering through a couple of simple sliders.
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- Remove false positives by clicking on them.
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## Getting Started
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- Install python (>=3.8 recommended... I made sure to explicitly use ordered dictionaries but just in case).
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- Install dependencies in whichever way you prefer.
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- Create the folders "in", "out" and "cache" (or run colonycounter.py).
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- Adjust queue functions in source code to suit your needs (and read through [Caveats](#caveats)).
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- Copy/Move your images into the "in" folder.
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- Start the program by running the colonycounter.py file.
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## Key Binds
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| Key | Function |
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|-----------------|----------------------------------------------------------------------------------------|
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| q, left arrow | load previous image |
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| w, right arrow | load next image |
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| a | apply changes (always do this before switching images, otherwise changes will be lost) |
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| r | reset changes that have not yet been applied |
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| l | load saved settings from disk |
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| s | save currently applied settings to disk |
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| left mouse btn | add colony to list of ignored colonies |
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| right mouse btn | remove colonies in the vicinity from ignore list |
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| c | clear list of ignored colonies |
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| e | batch process and export all images |
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## Caveats
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- The current processing queue expects 16bit gray scale images with the file extension .tif (tagged image file).
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- watershed function does not work on 16 bit images... so there are some hard coded values to bring measurements back to 16bit brightness values
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- this means a loss of resolution
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- To get hour and culture type values the following folder structure is expected:
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- "$DIRIN/OPTIONAL\_FOLDERS/$HOUR/$CULTURETYPE/image.tif"
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- $HOUR = integer followed by the letter h
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- $CULTURETYPE = whatever string identifies your culture type
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- Code documentation is currently lacking
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- Not all types are properly annotated
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