This code is based on the phagosight software, but modules for the analysis of overlapping cells within a video sequence have been added. For more detailed explanations, developer logs and explanations of routines, we are building a wiki.
To clone this repository use the following command:
git clone https://github.com/alonsoJASL/macrosight/To configure the paths automatically, inside Matlab, run the command
configureMacrosight. If you have @phagosight, then the configuration will
walk you through adding it to your path. Otherwise, you can choose not to use
it.
The best way to see Macrosight's functionalities is through the demos. In Matlab run
macrosight_demoto get a list of ready-made examples of the software functionalities:
macrosight_demo
[MACROSIGHT_DEMOS] Select the demo from the list:
[1] Select contact events - save to xls.
[2] Load from saved data - plot results
[3] Load from saved data - statistical analysis
[9] Demo tidy function
[C] Cancel
Your choice [default=1]:
Tracking needs PhagoSight, clone it with the command:
git clone https://github.com/phagosight/phagosight/and then in Matlab run configureMacrosight.
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 with the setup
function: setupInitialStructures.m.
The function allows the user to select an experiment and continue on a
previously loaded dataset.
[tablenet, clumptracktable, clumpidcodes, ~] = setupInitialStructures();Macrosight is an ongoing project at an early stage. We welcome all feedback and comments in the issues page.