Copyright © 2022 Oregon State University
Dominic W. Daprano Sheng Tse Tsai Moritz S. Schmid Christopher M. Sullivan Robert K. Cowen
Hatfield Marine Science Center Center for Qualitative Life Sciences Oregon State University Corvallis, OR 97331
This is a contribution to World Wide Web of Plankton Image Curation wwwPIC, a project funded by the Belmont Forum and the National Science Foundation (NSF award number 1927710).
This program is described in Panaïotis et al. 2022: Panaïotis T, Caray–Counil L, Woodward B, Schmid MS, Daprano D, Tsai ST, Sullivan CM, Cowen RK and Irisson J-O (2022) Content-Aware Segmentation of Objects Spanning a Large Size Range: Application to Plankton Images. Front. Mar. Sci. 9:870005. doi: 10.3389/fmars.2022.870005 https://www.frontiersin.org/articles/10.3389/fmars.2022.870005/full
This program is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
This program is distributed under the GNU GPL v 2.0 or later license.
Any User wishing to make commercial use of the Software must contact the authors or Oregon State University directly to arrange an appropriate license. Commercial use includes (1) use of the software for commercial purposes, including integrating or incorporating all or part of the source code into a product for sale or license by, or on behalf of, User to third parties, or (2) distribution of the binary or source code to third parties for use with a commercial product sold or licensed by, or on behalf of, User.
This tool allows for the segmentation of in situ footage of plankton imagery. The segment binary takes video files or images as inputs. The frames are flat-fielded using a vertical average and then regions of interest (ROIs) are extracted with the Maximal Stable Extrema Regions (MSER) algorithm. ROIs are segmented and their information saved (area, major_axis, minor_axis, etc) as the output of the program.
In order to build the project CMake 3.0.0, C++17, OpenCV 4.0.0, and OpenMP are all required.
This project has been successfully compiled with g++ 8.0+ on Ubuntu 20.04 and Centos 8.
To setup, first clone the repository.
cd Threshold-MSER
mkdir build
cd build
cmake ../
make
Now the binary can be run.
./segment --help
There are a few build options that can also be specified.
OpenMP can be disabled with the WITH_OPENMP=OFF flag in cmake.
cmake -DWITH_OPENMP=OFF ../
Additionally, the segmentation process can be observed by using the VISUAL_MODE=ON flag in cmake. If the project is built with VISUAL_MODE=ON it will automatically set WITH_OPENMP=OFF.
cmake -DVISUAL_MODE=ON ../
The only required parameter of segment is the input parameter. This can either be a path to a directory containing video files, a path to a video file, or a path to a folder of images.
./segment -i <path/to/dir>
The segments that are produced can be controlled through several parameters. Most notably, the --minium and --maximum paraters control the minimum and maximum size of a crop that can be extracted from a frame.