Hello people!
Community Bonding is considered as an important stepping stone in the GSoC timeline. This period allows the participants to become familiar with the working style of their chosen organization, along with its guidelines and rules. This comes as an excellent opportunity to network, learn more about developers, and their approach to writing code. So far, I have introduced myself and the project to the community mailing lists:
- https://sourceforge.net/projects/sbml/lists/sbml-spatial
- jsbml-development@googlegroups.com
Further, I have studied the documentation of the Spatial Processes package of SBML 3 in detail.
I have also started creating the dataset of segmented microscopic cellular images. The first step is to locate and identify sources of actual microscopic images. Some of these sources include
- http://www.cellimagelibrary.org/pages/datasets
- https://data.broadinstitute.org/bbbc/image_sets.html
- http://murphylab.web.cmu.edu/data/
As a next step, one needs to collect images that serve the purpose and then segment them using Fiji is Just ImageJ application. This app can be downloaded from http://fiji.sc/. Note to self: it is not the best idea to start running the imagej.exe directly from the downloaded folder. In such a case, it may show "Could not find ij.jar in C:\Users\.....\AppData\Local\Temp\TEMP3_~1.ZIP\Fiji.app/jars/" error. The trick is to create a new folder somewhere else on the computer (preferably Desktop), copy the contents, and then run the executable file.
I also tried to build the XitoSBML code but unfortunately faced some compilation errors. Hopefully, I will be able to run the code with some help from the mentors.
Until the next time
Adios!
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