fastER
Overview
fastER is an easy-to-use tool for ultrafast and robust detection of cell outlines in microscopy images (cell segmentation). It is orders of magnitude faster than existing software while producing state-of-the-art segmentation quality.
It supports various cell types and image acquisition modalities, but is easy-to-use even for non-experts: it has no parameters and can be adapted to specific image sets by interactively labelling cells for training.
See Instructions (below) for more information.
Instructions
Download a short guide how to use fastER:
DownloadfastER - Getting Started (PDF, 760 KB)
[alternative download link]
Download fastER
Download fastER binaries for Windows and Linux (for Windows users, we recommend to use the provided automatic installers) or C++ source code (can also be compiled for Mac):
Windows Installers (use right-click and save as):
DownloadfastER v1.3.5 - Installer - Windows (64 Bit) (MSI, 20.1 MB)
[alternative download link]
DownloadfastER v1.3.5 - Installer - Windows (32 Bit) (MSI, 18.2 MB)
[alternative download link]
Linux (binaries only):
DownloadfastER v1.3.5 - Binaries - Linux (64 Bit) (ZIP, 33 MB)
[alternative download link]
Source code:
Datasets
Brightfield images of murine HSPCs (with ground truth):
DownloadDataset BF (ZIP, 52 MB)
[alternative download link]
Synthetic fluorescence images (with ground truth):
DownloadDataset FL (ZIP, 24.9 MB)
[alternative download link]
Phase contrast images of HeLa cells originally from [1] (in .png format and with ground truth):
DownloadDataset PC (ZIP, 1.5 MB)
[alternative download link]
[external pageoriginal download location, .pgm format]
[1] Arteta, C., Lempitsky, V., Noble, J. A., and Zisserman, A. (2012). Learning to Detect Cells Using Non-overlapping Extremal Regions. In Medical Image Computing and Computer-Assisted Intervention, pages 348–356. Springer.
References
If you use fastER for your research, please cite the following paper:
Hilsenbeck O, Schwarzfischer M, Loeffler D, Dimopoulos S, Hastreiter S, Marr C, Theis FJ and Schroeder T (2017)
fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy
Bioinformatics, 33: 2020-2028
License
fastER is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details (external pagehttp://www.gnu.org/licenses/gpl-3.0.html).