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dc.contributor.authorHolst, Glendon
dc.contributor.authorBerg, Stuart
dc.contributor.authorKare, Kalpana
dc.contributor.authorMagistretti, Pierre J.
dc.contributor.authorCali, Corrado
dc.date.accessioned2017-01-02T09:55:27Z
dc.date.available2017-01-02T09:55:27Z
dc.date.issued2016-12-01
dc.identifier.citationHolst G, Berg S, Kare K, Magistretti P, Cali C (2016) Adding large EM stack support. 2016 4th Saudi International Conference on Information Technology (Big Data Analysis) (KACSTIT). Available: http://dx.doi.org/10.1109/KACSTIT.2016.7756066.
dc.identifier.doi10.1109/KACSTIT.2016.7756066
dc.identifier.urihttp://hdl.handle.net/10754/622512
dc.description.abstractSerial section electron microscopy (SSEM) image stacks generated using high throughput microscopy techniques are an integral tool for investigating brain connectivity and cell morphology. FIB or 3View scanning electron microscopes easily generate gigabytes of data. In order to produce analyzable 3D dataset from the imaged volumes, efficient and reliable image segmentation is crucial. Classical manual approaches to segmentation are time consuming and labour intensive. Semiautomatic seeded watershed segmentation algorithms, such as those implemented by ilastik image processing software, are a very powerful alternative, substantially speeding up segmentation times. We have used ilastik effectively for small EM stacks – on a laptop, no less; however, ilastik was unable to carve the large EM stacks we needed to segment because its memory requirements grew too large – even for the biggest workstations we had available. For this reason, we refactored the carving module of ilastik to scale it up to large EM stacks on large workstations, and tested its efficiency. We modified the carving module, building on existing blockwise processing functionality to process data in manageable chunks that can fit within RAM (main memory). We review this refactoring work, highlighting the software architecture, design choices, modifications, and issues encountered.
dc.description.sponsorshipThis work was supported by CRG3 KAUST grant
dc.publisherInstitute of Electrical and Electronics Engineers (IEEE)
dc.relation.urlhttp://ieeexplore.ieee.org/document/7756066/
dc.subjectcode refactoring
dc.subjectimage analysis
dc.subjectsegmentation
dc.subjectblockwise carving
dc.subjectlarge data
dc.titleAdding large EM stack support
dc.typeConference Paper
dc.contributor.departmentKAUST Visualization Laboratory (KVL)
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.identifier.journal2016 4th Saudi International Conference on Information Technology (Big Data Analysis) (KACSTIT)
dc.contributor.institutionHHMI Janelia Research Campus Virginia, United States
kaust.personHolst, Glendon
kaust.personKare, Kalpana
kaust.personMagistretti, Pierre J.
kaust.personCali, Corrado


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