SIAL

Simple Image Analysis Library

SIAL: A simple image analysis library for wet-lab scientists

David R. Tyrpak ¹, Yaocun Li ¹, Siqi Lei ¹, J.A. MacKay ^1,2,3

1 Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, 1985 Zonal Ave, Los Angeles, CA, USA 90089

2 Keck School of Medicine of the University of Southern California, Department of Ophthalmology, Roski Eye Institute. 1450 San Pablo St, Los Angeles, CA, USA 90033

3 University of Southern California Viterbi School of Engineering, Biomedical Engineering. 1042 Downey Way, Los Angeles, CA, USA 90089

Summary:

In many biomedical research labs, image analysis tasks are relatively simple but labor intensive. For example, a typical workflow may require human intervention to outline regions of interest or score phenotypes from a collection of images. Such tasks could potentially be partially automated with a script or machine learning, but in our experience, many biomedical researchers do not obtain programming skills. Furthermore, image analysis is typically just one of the many experiments that a busy researcher will employ during the course of a project, and so devoting time to learning programming or bespoke image analysis is not prioritized. These factors create an unfortunate situation where, in addition to being labor intensive, image analysis workflows may become biased and exhibit limited reproducibility.

As primarily “wet-lab” scientists, we wanted to develop user friendly programs focused on the most common tasks that fellow wet-lab researchers encounter during image analysis. Because FIJI/ImageJ is routinely used by biomedical researchers the world over, we developed our programs in Java and packaged them together as a FIJI plugin. We name this plugin SIAL: A simple image analysis library. SIAL aids users in human-assisted image analysis by providing programs for image pseudonymization, phenotype scoring, and ROI harvesting. Each of the three programs inside SIAL is briefly summarized below:

File Randomizer: This program provides a convenient way for researchers to pseudonymize their imaging data, which is a critical step in any analysis involving phenotype scoring or ROI selection. The program copies images in a specified input directory to a specified output directory, and then randomly renames the copied images with a three-digit number. It also outputs a key matching the original filenames to the renamed images and a details file which records time of analysis, as well as the specified input and output directory. Note that the File Randomizer does not provide anonymization of the input data; it provides pseudonymization, since the generated key file retains the information neccesary to re-identify the original file names of the randomly renamed images.

PhenoScoreKeeper: This program helps speed up manual phenotype scoring of images by partially automating score collection. Users specify an input directory and output directory, and the program automatically opens up each image in the input directory and prompts the user to enter an integer score for the image. It saves the scores in a csv file located in the specified output directory.

ROI Recorder: This program uses ImageJ's built-in ROI manager to quickly harvest ROIsets and measurements from images in a specified input directory. The program opens up the input images one at a time and prompts the user to harvest ROIs. It then automatically saves the ROIsets and ROI measurements for each image to the specified output directory.

Both the PhenoScoreeKeeper and ROI Recorder programs track which images have already been analyzed so that users can stop and start their analyses without losing progress. Links to videos detailing the use of these programs are provided in the Installation and Tutorials section.

SIAL is easily installed via the ImageJ update website service, utilizes simple user interfaces, requires no programming experience, and requires no dependencies except FIJI. The individual programs inside SIAL can be easily integrated with workflows involving other FIJI plugins or with workflows employing another open source software, like Cell Profiler or QuPath. Because of its ease of use and focus on the most common wet-lab image analysis tasks, SIAL is routinely used by our group and our close collaborators to improve the efficiency and reproducibility of our image analysis workflows.

Author contributions:

SIAL was developed by David R. Tyrpak at the MacKay lab in the School of Pharmacy of the University of Southern California. Yaocun Li and Siqi Lei tested the software and reported bugs.

Acknowledgements:

This work was supported by grants RO1 GM114839 to JAM and F31DK118881 to DRT. We thank Anh Truong for valuable suggestions in improving the plugin. In addition, we also thank the image.sc community for technical assistance and advice.

Installation and Tutorials

First ensure you have FIJI installed on your computer: https://fiji.sc

To download SIAL, open FIJI, go to “Help > Update…” and then update FIJI. After FIJI is finished downloading all updates, a window named “ImageJ Updater” will open. Select “Manage Update Sites > Add update site” and add this url: https://sites.imagej.net/D-tear/

Be sure to check the box next to this update site to ensure the FIJI adds SIAL to your FIJI Plugins folder. Select “Close > Apply changes”. FIJI will download SIAL.jar and associated dependencies. After successfully updating, FIJI will then ask to be closed and restarted. After doing this, SIAL can be accessed via the Plugins tab in FIJI. Note that SIAL will usually be installed towards the bottom of the available FIJI plugins.

Links to YouTube tutorials covering the installation and use of SIAL:

Installing SIAL: https://youtu.be/RU4B3GhVwaM

How to use the File Randomizer program inside of SIAL: https://youtu.be/_oQLJ5gC7ls

How to use the PhenoScoreKeeper inside of SIAL: https://youtu.be/FiaNubIDvSw

How to use the ROI Recorder program inside of SIAL: https://youtu.be/9mTHGVeWJA0

How to import ImageJ/FIJI ROIs into QuPath: https://youtu.be/hCFrk9NJ4gk

Contact Info and Support

For software support and general questions about SIAL, including opportunities to contribute to SIAL, users should contact David Tyrpak at davidtyrpak31@gmail.com