Installing CiliaQ

System requirements

CiliaQ is a plugin for ImageJ and thus, it requires the installation of ImageJ (tested on versions 1.51n, 1.51r, 1.51u, 1.52i) or the ImageJ distribution Fiji on your computer (see below).

Hardware requirements

ImageJ/FIJI does not require any specific hardware and can also run on low-performing computers. However, a RAM is required that allows to load one image sequence that you aim to analyze into your RAM at least twice. ImageJ does not require any specific graphics card. The speed of the analysis depends mainly on the processor speed. Only the generation of 3D visualizations, an optional function of CiliaQ, will use the graphics card of the computer.

Operating system

The ImageJ plugins were developed and tested on Windows 8.1, Windows 10, and macOS Catalina (version 10.15.6). ImageJ is also available for Linux operating systems, where the ImageJ plugins and Java software in theory can be equally run.

Installing FIJI / ImageJ to your computer

ImageJ/FIJI is open-source, freely available software that can be downloaded here. If all your images to be analyzed are .tif files, we recommend you to use a pure "ImageJ" for the CiliaQ analysis, since CiliaQ is slightly faster on ImageJ than on FIJI. If your images are stored as "raw" microscopy files (e.g., ".oib", ".czi", ".nd2", ".lif"), you should use FIJI (at least for CiliaQ Preparator) since when used in FIJI CiliaQ Preparator can read these custom microscopy file formats using FIJI's Bioformats integration.

To install ImageJ / FIJI, you only need to download the distribution of your choice and fitting to your Operating system and extract the software directory from the downloaded archive.

On Mac OS, do not place the ImageJ / FIJI application into the "Applications" folder. Instead place it somewhere else than in the Applications folder, i.e. to the desktop or the documents directory. Thereby you can avoid an issue that might otherwise appear later.

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Installing CiliaQ

Once you have an instance of FIJI or ImageJ running on your computer, you can install CiliaQ. There are two ways for installing CiliaQ:

1. Via the update manager of FIJI / ImageJ2. To do this scroll down to heading 1. or click here
2. Manual installation in a pure ImageJ or if your FIJI / ImageJ2 cannot access the internet. To do this scroll down to heading 2. or click here.

1. Installing CiliaQ to FIJI / ImageJ2

Since December 2022, CiliaQ can be simply installed through FIJIs update manager. This also ensures that you always get the latest CiliaQ release when you update your FIJI / ImageJ2. Pursue the installation as follows:

• Go to the menu entry Help > Update in your FIJI.

• A dialog pops up that loads update site information - wait for it to complete.

• When it completed it will automatically close and open the following dialog (note that if you haven't updated your FIJI for a long time here may be a lot of updates listed - this is no problem you can just update everything along with installing CiliaQ so just continue with the following descriptions).

• Press OK in the "Your ImageJ is up to date"-message (if the message is displayed)
• Click "Manage Update Sites". This will open another dialog, in which you need to check two boxes: First, the "3D ImageJ Suite" update site (to use Hysteresis thresholding in CiliaQ Preparator) and second, the "CiliaQ" update site (you find it by scrolling down). Afterwards, press "Close".

• Now, in the original update dialog you will see new modules added for installation. Click "apply changes".

• The installation process may take some time, depending on the download speed.

• The installation process terminates with the following dialog:

• Close FIJI and restart FIJI.

• You can now verify that the "3D Suite" and "CiliaQ" are installed.

  • To check that the 3D suite is installed, verify that the menu entry Plugins > 3DSuite is available.
  • To check that CiliaQ is installed, verify that the menu entry Plugins > CiliaQ is available.

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2. Installing CiliaQ to a pure ImageJ / installing CiliaQ manually

Use these installation instructions if ...

• you use a pure ImageJ, which does not include the update manager
• you cannot access the internet from your FIJI/ImageJ distribution
• you do not want to use the update manager

Perform the installation as follows (we also show this type of installing CiliaQ in a video tutorial on YouTube - note, however, that the video is not fully up to date while the written guide is more up to date):

• Download the ImageJ plugins directly from the release pages of the individual repositories - Download the latest releases and download only the .jar files from these releases:
  • CiliaQ_Preparator
  • CiliaQ_Editor
  • CiliaQ

• Launch ImageJ and install the plugins by drag and drop into the ImageJ window (red marked region in the screenshot below)

• Confirm the installations by pressing save in the upcoming dialog(s).

• Next, ImageJ requires to be restarted (close it and start it again)

• Some functions (Hysteresis thresholding, Canny3D) in CiliaQ_Preparator require additional installation of the '3D ImageJ Suite' to your FIJI / ImageJ distribution. To install the 3D ImageJ Suite, do the following:

  • Download the core .jar and the plugin .jar file provided on this webpage from 3D ImageJ Suite's download section and install them to your FIJI / ImageJ by drag and drop into the FIJI / ImageJ window.
  • NOTE: The webpage for download is external and has been changing over the last years. If the webpage looks awkward, check the '3D ImageJ Suite' forum entry to see where the webpage has been moved.

• You can now verify that the "3D Suite" and "CiliaQ" are installed.

  • To check that the 3D suite is installed, verify that the menu entry Plugins > 3DSuite is available.
  • To check that CiliaQ is installed, verify that the menu entry Plugins > CiliaQ is available.