Added readme.

README.md

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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