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Dragonfly_AstrocyteMacro

A Macro in Dragonfly to prune automatically annotated astrocyte volumes

The following instructions will allow you to install this macro across any new computer.

  1. Press [Windows Key] + [R] and search "AppData"

  2. Search for "Local" folder

  3. Search for "ORS" folder

  4. Search for "DragonflyXXXX.X" folder

  5. Search for "pythonUserExtensions" folder

  6. Search for "Macros" folder

  7. Place the 3 macros downloaded from this github into this folder.

  8. KEEP THIS FOLDER OPEN WHILE YOU DO STEPS 9 - 17

  9. Open Dragonfly Program

  10. Navigate to the "Utilities" tab

  11. On the drop down, click "Start Command Prompt"

  12. In the Command Prompt, type "pip install opencv-python"

  13. Close and reopen dragonfly once the python package has been installed

  14. Navigate to the "Artificial Intelligence" tab

  15. On the drop down, click "Deep Learning Tool"

  16. Right click your model of interest, and select "Open Model Folder in File Browser"

  17. At the top of your file browser, click the "models" folder that comes right before the specific network model folder you are in. You should have navigated from this: C:\ProgramData\ORS\DragonflyXXXX.X\pythonAllUsersExtensions\PythonPluginExtensions\DeepTrainer\models\SpecificNetworkModel_XXXXXXXXXXXXXXXXXXXXX to this: C:\ProgramData\ORS\DragonflyXXXX.X\pythonAllUsersExtensions\PythonPluginExtensions\DeepTrainer\models

  18. Once you are in the model folder, identify your astrocyte model folder.

  19. Right click the astrocyte model folder, and click "Rename"

  20. DO NOT CHANGE THE NAME OF THE FOLDER, copy and paste the name of the folder into a seperate text file. (e.g. ExampleModelFolder_73dae9de648c11eb93d300d8615a0557)

  21. Repeat steps 14-16 for your mitochondria model folder.

  22. RETURN TO "AppData/Local/Ors/Dragonfly/pythonUserExtensions/Macros" FROM STEP 8

  23. Open "SegmentAstrocytefromVolumev2_XXXXXXXX.py" with a text editor (notepad is fine)

  24. Navigate to line 68

image

  1. Paste only the UID of the astrocyte folder and mitochondria folder into the quotation marks

image

  1. Save the python file
  2. Open dragonfly and test macro!