Installation ( Linux )

Update the dependency tree.

sudo apt update

Install npm and node.js to download and execute the preprocessor.

sudo apt install nodejs npm build-essential imagemagick -y

Install the preprocessor globally so you can use it everywhere.

npm install -g baubiologie-preprocessor

Installation ( Windows )

Install ImageMagick that performs the detection for blurry images.

Install Node.js for the executable and file system operation.

Open CMD and use this command to install the program.

npm install -g baubiologie-preprocessor

Update the installation

Open CMD and use this command to update the program.

npm update -g baubiologie-preprocessor

Usage

General

The source folder holds the original .tif images and the destination folder holds the .png output.

preprocessor <microscope> <source> <destination> <quality/remove>

microscope : One of ['zeiss','free'] source : 'image' destination : 'output' quality/remove: If microscope == free then see #Quality If microscope == zeiss then see #Remove

Quality

The preprocessor can set different levels of image quality

preprocessor free images output 92

Quality is 1 (lowest image quality and highest compression) to 100 (best quality but least effective compression). The default is to use the estimated quality of your input image if it can be determined, otherwise 92.

Remove

The preprocessor can be set to remove the old images for the zeiss microscope

preprocessor zeiss images output yes

A short yes at the end will remove all files

Example

A working example ( Linux )

preprocessor zeiss ./images/ ./output/ yes

A working example ( Windows )

preprocessor zeiss images output