MIST ·

What is MIST?

Microscopy Image Stitching Tool (MIST), is a stitching tool for 2D grids of images. MIST estimates the stage mechanical model (actuator backlash, stage repeatability ‘r’, etc.) from computed pairwise translations and then minimizes stitching errors by optimizing the translations within a (4r)^2 square area. This minimizes the maximum uncertainty related to the translation computation for any pair of images.

Summary

With new microscope technologies, scientists are acquiring terabyte-sized datasets to cover large area of their experiments. An automated optical microscope acquires images of a cell cultures specimen. The microscope acquires a grid of partially overlapping images because the microscope field of view is much smaller than the dimensions of the specimen being imaged. This process generates hundreds of thousands of images that need to be stitched into a large mosaic to derive meaningful information. Some of these large mosaics are sparse, mainly at the beginning of an experiment before cells grow and cover more areas. This creates overlapping areas with no foreground pixel intensities to compute the translations between tiles, which increases the translation computation uncertainty for the entire mosaic. Moreover, stitching such large image mosaic is computationally taxing; this becomes overwhelming for live cell experiments.

Staff:

ITL - Software and Systems Division

Information Systems Group

University of Maryland, College Park

Fischell Department of Bioengineering

Kiran Bhadriraju

Publications:

J. Chalfoun, M. Majurski, T. Blattner, W. Keyrouz, P. Bajcsy, and M. C. Brady, “MIST: Accurate and Scalable Microscopy Image Stitching Method with Stage Modeling and Error Minimization,” Scientific Reports, vol. 7, no. 1, 2017, DOI: 10.1038/s41598-017-04567-y
(view article)

J. Chalfoun, "A power stitching tool", SPIE Newsroom, 2014, DOI: 10.1117/2.1201402.005365
(download pdf) (view article)

T. Blattner et. al., "A Hybrid CPU-GPU System for Stitching of Large Scale Optical Microscopy Images", 2014 International Conference on Parallel Processing, 2014
(download pdf) (view article)

Collaborators:

MML-Biosystems and Biomaterials Division

Anne Plant

Cell System Science Group

John Elliott

Features

2D+Time+Channel Image Stitching
Hybrid Workflow Implementation
Multi-CPU and Multi-GPU
Handles TBs of Data
Real-Time Stitching
Memory Efficient
Fiji/ImageJ Plugin
Open Source

Example Datasets

MIST has been applied to large and diverse datasets in terms of content, imaging modalities, and microscopes; totaling over a thousand fully stitched images. The stitched datasets have been acquired using five microscopes (Leica, Olympus, Nikon, Focused Ion Beam Scanning Electron Microscope (FIB-SEM), and Zeiss), four different imaging modalities (fluorescent, phase contrast, bright-field, and FIB-SEM), a range of image overlaps, and a large range of grid sizes (5x5 to 300x300).

MIST application example images: (1) A10 cells, (2) Carbon Nanotubes, (3) HBMSC, (4) IPS cell colonies, (5) Paper nanoparticle, (6) Rat brain cells, (7) Stem cell colonies, and (8) Worms.

MIST has stitched eight different content types: (1) A10 cells, (2) Carbon Nanotubes, (3) HBMSC, (4) IPS cell colonies, (5) Paper nanoparticle, (6) Rat brain cells, (7) Stem cell colonies, and (8) Worms.

Application Domain

2D Grid of Images + Time Series + Multiple Image Modalities

MIST was designed to perform 2D time-sequence multichannel stitching. It cannot perform volumetric stitching (3 spatial dimensions) which requires a system to identify and correlate features across a third dimension (e.g., Z-axis). However, MIST can stitch a numbered series of independent image grids, for example, a time-series of image grids. Additionally, MIST also handles datasets that can use the same image positions, such as stitching multiple channels, using the assemble from metadata functionality.

License

NIST-developed software is provided by NIST as a public service. You may use, copy and distribute copies of the software in any medium, provided that you keep intact this entire notice. You may improve, modify and create derivative works of the software or any portion of the software, and you may copy and distribute such modifications or works. Modified works should carry a notice stating that you changed the software and should note the date and nature of any such change. Please explicitly acknowledge the National Institute of Standards and Technology as the source of the software.

NIST-developed software is expressly provided "AS IS." NIST MAKES NO WARRANTY OF ANY KIND, EXPRESS, IMPLIED, IN FACT OR ARISING BY OPERATION OF LAW, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT AND DATA ACCURACY. NIST NEITHER REPRESENTS NOR WARRANTS THAT THE OPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR-FREE, OR THAT ANY DEFECTS WILL BE CORRECTED. NIST DOES NOT WARRANT OR MAKE ANY REPRESENTATIONS REGARDING THE USE OF THE SOFTWARE OR THE RESULTS THEREOF, INCLUDING BUT NOT LIMITED TO THE CORRECTNESS, ACCURACY, RELIABILITY, OR USEFULNESS OF THE SOFTWARE.

You are solely responsible for determining the appropriateness of using and distributing the software and you assume all risks associated with its use, including but not limited to the risks and costs of program errors, compliance with applicable laws, damage to or loss of data, programs or equipment, and the unavailability or interruption of operation. This software is not intended to be used in any situation where a failure could cause risk of injury or damage to property. The software developed by NIST employees is not subject to copyright protection within the United States.

MIST