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Welcome to the macrosight wiki!
This code is based on the phagosight software, but modules for the analysis of overlapping cells within a video sequence have been added.
To clone this repository use the following command:
git clone https://github.com/alonsoJASL/macrosight/This will not have all functionalities, as @phagosight is necessary to run it.
You need to clone PhagoSight as "recursive", which will pull macrosight as a submodule.
git clone --recursive https://github.com/alonsoJASL/phagosight/At the moment, you will be pulling my fork of the original @phagosight.
To configure the paths automatically, inside Matlab Run the command configureMacrosight.
The macrophages dataset need to be in individual files, with the following naming convention:
/path/to/data/MACROSN/T000ix.tifwhere N corresponds to the nth experiment and ix correspond to each image's
identifier.
Functionalities will soon be included to prepare the data automatically.
Macrosight takes images stored in a hard drive, and saves the output to other folders following a specific naming scheme.
For segmentation, see the file preinit_segmentation.m.
This script arranges the data into the cooresponding output folders
_data_Ha_data_Re_data_La
Tracking and inclusion of clump information, is done in the initialisation
file: initscript.m. The file allows the user to select an
experiment and continue on a previously loaded dataset.
Macrosight is an ongoing project at an early stage. We welcome all feedback and comments in the issues page.
Also, please notice that this research is ongoing, so bugs are likely to appear. Some of the functions might not be present, because they are part of another package that has not been uploaded or linked to macrosight. If you are thinking of using our code, please feel free to submit any issues to the issues page, so that small bugs are dealt with.