Concurrent Scientific Session (Imaging): Open Mic
Steps towards providing mouse behavior analysis across multiple core facilities
Our Light Microscopy Core has been collaborating with our Mouse Behavior Core to set-up workflows to provide quantitative image analysis (in the Microscopy Core) on behavioral videos (collected within the Behavior Core). In doing so, we have encountered some unexpected aspects to consider, specifically regarding compensation for work, reporting work/usage, sharing of data and MTAs, and delivering consistent and robust quantitative results to users. We are interested in discussing solutions and work arounds that we are discovering and ways that other Facilities have successfully managed to implement cross-core analysis and workflows. We are also interested in discussing ways to make advanced image analysis procedures that rely on maximum likelihood models more reproducible and standardized in their results either via training or insertion of 'known' or 'stereotyped modules' into the analysis.
Serial block face imaging
We have recently installed a serial block face imaging system and have collected our first major data set. The project was a proof of concept to track the progress of pollen tubes towards specialist cells involved in plant reproduction. Pollen tubes target synergid cells and in particular the basal membrane of those cells which is known as the filiform apparatus. Little to nothing in known about the behavior of the filiform apparatus during pollen tube reception. By examining the ovules of Arabidopsis in 3D volumes we hope to examine whether the pollen tube enters the receptive synergid through the filiform apparatus, In addition we hope to determine if the pollen tube enters the receptive synergid at all. We prepared samples using an enhanced protocol that has been designed to improve signal and contrast in samples for serial block face imaging. We collected close to 1800 40nm slices from 3 different regions. We successfully found and oriented the two synergids in different ovules. We used Amira for visualization and have carried out segmentation of the filiform apparatus.
Challenges of Establishing a new imaging facility: The floating core diaries
Core facilities are an essential resource in research institutes. They provide dedicated expertise and the instrumentation necessary for the development and improvement of science in academia. However, establishing a new microscopy core facility in a competitive environment like Harvard Medical School is not extent of challenges. In most cases it requires the creation of dedicated spaces, which are hard to come by and/or expensive to renovate, to host the instruments, and attracting users to obtain a solid user base is essential for the success of the core. Our imaging core, MicRoN, was created as a decentralized or floating core. Microscopes from different departments and from individual labs are managed and maintained by the core, but hosted in their original locations: 6 different microscopy rooms embedded within three departments at Harvard Medical School. This approach leverages the existing departmental microscopes that are traditionally poorly maintained and lab-owned, which tend to be under-utilized and lack necessary upgrades. Importantly, the decentralized core generates greater interaction among trainees from the different Departments and encourages a more collaborative environment. We believe our example serves as a new model for how Departments and Institutions can create an imaging core with a relatively modest initial investment.