PINNA-2D

PINNA 2D - Pixel-wIse NeuroN Annotation

Installation

Ubuntu: download Pinna_unix_0_1.sh, install and run

Mac: download Pinna_macos_0_1.dmg, and run the dmg directly

Download the JAR download PINNA-2D-0.1-jar.jar and run

java - jar PINNA-2D-0.1.jar

if you get javafx not found related bug install Javafx in ubuntu by:

sudo apt install openjfx

Usage

Initiate Project

1- Specify the project folder:

Everything related to the project will be saved there. ( The database, the CSV statistic of cells with space dims, the instance classification images ).

2- Specify the RAW tiff folder:

The folder where there are the tiff files.

3- Specify the Masks tiff folder:

The folder where there are the masks files. You can download them from masks.zip

4- Specify the LUT file:

The LUT is the file used to color the cells in the view. You can download them from glasbey_inverted.lut

5- Start the process:

Click SCAN to detect all the files. if everything is ok, select the file you want to analyze and click Next.

Classify the cells

You have just to select the cell you want to annotate from the list or from the image. Then you select the right category. After annotating the full image, you can export the statistic as CSV and the image of the classification. The image will be used to train the model.

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update the tests as appropriate.

PreibischLab / PINNA-2D