Quick start


With the WebMicroscope Compressor, image files produced by slide scanners can be very efficiently compressed, while still preserving image quality. As the wavelet file format is optimized for ultra fast reading on a web server, server costs can be cut both by reduced requirements on both disk space, and processing power.

  • Automatically detects and compresses new scans
  • Reads multiple scanner file formats
  • Highly effective wavelet compression

Fig 1. Overview schema of a virtual microscopy system setup. Click to view as pdf.

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Quick start

  1. Unzip and run the Setup Wizard
  2. Install also the Slide AC application from 3DHistech if you will be using a 3DHistech
    slide scanner (.mrxs files)
  3. Launch the WebMicroscope Compressor
  4. Configure the Input folder, i.e. the folder to watch for new scanned slides
  5. Configure the Output folder, i.e. the folder where you want the compressed slides to appear
  6. Click the Start button - the Compressor will check the folder for new scans every minute

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Software: The WebMicroscope Compressor runs on a PC/Windows computer (Windows 7 or Windows 8). Both 32 and 64 bit versions are available. The 64 bit version is recommended.

In order to compress virtual slides from a 3DHistech scanner, you must install the "Slide AC" sofware from 3DHistech. Please contact us for more information. 3DHistech provides the software in both 32 and 64 bit versions.

Hardware: Minimum is a dual core processor. For each additional CPU core, one parallel process can be run (if needed). Free disk space to store the compressed files on, (approx 0.5 Gb/slide with 0.22 um/px resolution)

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To install the WebMicroscope Compressor, extract the contents of the zip file to your computer (if delivered in a zip archive), and double click the Setup file. This will launch the Setup Wizard (Figure 2-4)

Fig 2. The first step in the Setup Wizard.

Fig 3. The second step in the Setup Wizard. You can choose if the application will be installed only for you,
or for all users on the computer.

Fig 4. In the third step you can make the Compressor launch with Windows.

Fig 5. The last step of the Setup Wizard. Click Close to finalize the installation.

After installation the compressor can be launched from the desktop icon, Start menu on Windows 7 (Fig 6), or Start screen on Windows 8.

Fig 6. Start menu entry on Windows 7.

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The WebMicroscope Compressor interface is seen in Figure 7.

Fig 7. The WebMicroscope Compressor interface.

Input folder: The folder to watch for new scanned slides. It can be a local folder, for example c:\scans, or a LAN folder, for example \\scanner\newslides

Incl subfolder: If this is checked, the Compressor will monitor also subfolders of the Input folder.

Login: If the Compressor needs to login to a LAN folder, you can enter credentials here.

Output folder: The folder where you want the compressed slides to appear.

Copy to: If you want a copy of the output to go also to another folder you can enter the address here. This could be for example a Server folder, Backup station folder, or a Sync folder for cloud uploading

Login: If the Compressor needs to login to a LAN output folder, you can enter credentials here.

Make ecw with compression rate: The ecw (Enhanced Compressed Wavelet) format is the default, and recommended format. It is highly efficient, and decompresses ultra fast on the server. By entering a higher number (default 16), the slides will be more compressed, saving disk storage costs. The checkbox should be checked.

Make jp2 with compression rate: The jp2 (JPEG2000) format is also a wavelet format. It is highly efficient, but does not decompress as fast as ecw on servers. By entering a higher number (default 20), the slides will be more compressed, saving disk storage costs

Folder specific rate: It is possible to configure compression rates separately for each input folder. These values will then override the general settings enterd in the user interface.

Nr of parallel processes: If your computer has a multi core processor, you can increase the number of processes to run in parallel. Set the number to match the number of cores, or 1-2 below.

Executable: This is an advanced option. Does not need to be configured.

Settings: You can store 2 sets of settings.

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