StitchIt is a MATLAB package that was originally built for stitching data from the TissueVision 2-photon tomography system. However, StitchIt is now sufficiently modular that it can handle other tiled data sets too (e.g. from a slide scanner or tiled images obtained from in vivo experiments using ScanImage). To get started, please read the Wiki. Some older information is for now only available in the PDF user manual. There is a changelog.
With a single command (
syncAndCrunch) the user can:
- Pre-process image tiles as they are being acquired.
- Display the last acquired section on the web.
- Automatically stitch data when acquisition completes.
- Send Slack notifications when acquisition completes or pre-processing fails.
- Automatically conduct arbitrary analyses after acquisition completes.
StitchIt has commands for basic tasks such as:
- Stitching subsets of a data set.
- Calculating the average tile for illumination correction.
- Calculating coefficients for correcting for scanning artifacts (experimental).
- Randomly accessing any tile in the dataset.
- Techniques for exploring stitching accuracy.
- Correction of intensity differences across different optical sections.
- Removal of tile seams in stitched images.
- Down-sampling the dataset to a single multi-page TIFF stack or MHD file.
Clone the repository. Add the
code directory and its sub-directories to your MATLAB path. In addition, you will need
to acquire the following and add to your MATLAB path:
- Slack MATLAB
- YAML MATLAB
- rsync is needed if you want to use the
syncAndCrunchtool to process data during acquisition.
- Additionally, you will need the following MATLAB toolboxes: statistics, parallel computing, and image processing.
Questions and bug reports
Please use the project's issue tracker for questions, bug reports, feature requests, etc.
This software is distributed under the GPL v3 licence. This repository may be freely forked and shared so long as this licence is attached.