SHERPA - Shape Recognition, Processing and Analysis
SHERPA is a software tool developed by Michael Kloster implementing a highly customizable image processing workflow for the identification and quantification of object outlines. SHERPA was mainly developed for the analysis of bright field microscopic images of diatom valves but might be useful for other applications as well.
When using SHERPA for your research, please cite our publication describing it:
Kloster M., Kauer G. & Beszteri B. (2014): SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects. BMC Bioinformatics 15:218.
Here are our publications using SHERPA:
Kloster, M., Kauer, G., Esper, O., Fuchs, N. and Beszteri, B. (2018). Morphometry of the diatom Fragilariopsis kerguelensis from Southern Ocean sediment: High-throughput measurements show second morphotype occurring during glacials. Marine Micropaleontology 143: 70-79.
Beszteri, B., Allen, C., Almandoz, G.O., Armand, L., Barcena, M. A., Cantzler, H., Crosta, X., Esper, O., Jordan, R. W., Kauer, G., Klaas, C., Kloster, M., Leventer, A., Pike, J. and Rigual Hernández, A.S. (2018). Quantitative comparison of taxa and taxon concepts in the diatom genus Fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy. Journal of Phycology 54: 703-719.
Kloster M., Esper O., Kauer G. & Beszteri B. (2017):Large-Scale Permanent Slide Imaging and Image Analysis for Diatom Morphometrics. Applied Sciences 7(4): 330.
SHERPA is provided for your use for free but without any guarantees, please read the below disclaimer before downloading.
THE SOFTWARE AVAILABLE HERE IS PROVIDED ''AS IS'' AND ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL AWI OR ITS STAFF BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT INCLUDING NEGLIGENCE OR OTHERWISE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
New version SHERPA 1.1c available:
Microsoft .NET Framework 4.62, the Microsoft Visual C++ 2010 SP1 Redistributable Package (x64) and the Microsoft Visual C++ Redistributable for Visual Studio 2012 Update 4 (x64) (please download file "VSU_4\vcredist_x64.exe") are required for running SHERPA 1.1c (if not already present on your system).
Old version SHERPA 1.0:
Microsoft .NET Framework 4 and the Microsoft Visual C++ 2010 SP1 Redistributable Package (32 bit / 64 bit) are required for running SHERPA 1.0 (if not already present on your system).
Example images for testing SHERPA: a typical sample of Fragilariopsis kerguelensis valves from sediment core PS1768-8 (the slide was kindly provided to us by Rainer Gersonde). The original high resolution TIFs are available from PANGAEA.
R code for Sellaphora analyses of images from Mann et al. (2004).
