Broad Institute Visit , 28-29th July 2010, Anne Carpenter’s lab
Pauli Raemoe from Lucas Pekmans’ lab at the ETH and myself visited Anne and her team. Anne’s team is developing Cell Profiler and Cell Profiler Analyst. Those tools are used to process large batches of cell images. Pauli presented iBRAIN and Cell Classifier and I gave a talk on SyBIT, openBIS and iBRAIN, which included demos. We were given demos of Cell Profiler and Cell Profiler Analyst, and discussed the software architecture in detail. The current challenge to Cell Profiler seems to be in cell tracking, for which ImageJ may be used.
We will collaborate with the Broad Institute in developing our tools further, to support data flow between all the relevant applications. The modular nature of the systems and the use of web data protocols make this feasible. There was significant interest in openBIS, and the question to be decided is how much image viewing is supported in Cell Profiler Analyst and how much in openBIS. Similarly, integration with graph drawing software can be done in either Cell Profiler (or Analyst) or in openBIS. Further discussions will decide on how best to integrate the toolsets. We envisage sharing wiki links and lists of to-do items, to maximize benefits to both sides.
Categories: Trip Reports