BigDataProcessor2 : A free and open-source Fiji plugin for inspection and processing of TB sized image data
(2021) In Bioinformatics 37(18). p.3079-3081- Abstract
SUMMARY: Modern bioimaging and related areas such as sensor technology have undergone tremendous development over the last few years. As a result, contemporary imaging techniques, particularly electron microscopy (EM) and light sheet microscopy, can frequently generate datasets attaining sizes of several terabytes (TB). As a consequence, even seemingly simple data operations such as cropping, chromatic- and drift-corrections and even visualisation, poses challenges when applied to thousands of time points or tiles. To address this we developed BigDataProcessor2-a Fiji plugin facilitating processing workflows for TB sized image datasets.
AVAILABILITY AND IMPLEMENTATION: BigDataProcessor2 is available as a Fiji plugin via the... (More)
SUMMARY: Modern bioimaging and related areas such as sensor technology have undergone tremendous development over the last few years. As a result, contemporary imaging techniques, particularly electron microscopy (EM) and light sheet microscopy, can frequently generate datasets attaining sizes of several terabytes (TB). As a consequence, even seemingly simple data operations such as cropping, chromatic- and drift-corrections and even visualisation, poses challenges when applied to thousands of time points or tiles. To address this we developed BigDataProcessor2-a Fiji plugin facilitating processing workflows for TB sized image datasets.
AVAILABILITY AND IMPLEMENTATION: BigDataProcessor2 is available as a Fiji plugin via the BigDataProcessor update site. The application is implemented in Java and the code is publicly available on GitHub (https://github.com/bigdataprocessor/bigdataprocessor2).
(Less)
- author
- Tischer, Christian ; Ravindran, Ashis ; Reither, Sabine ; Chiaruttini, Nicolas ; Pepperkok, Rainer and Norlin, Nils LU
- organization
- publishing date
- 2021-02-17
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Bioinformatics
- volume
- 37
- issue
- 18
- pages
- 3079 - 3081
- publisher
- Oxford University Press
- external identifiers
-
- pmid:33594413
- scopus:85108556351
- ISSN
- 1367-4803
- DOI
- 10.1093/bioinformatics/btab106
- language
- English
- LU publication?
- yes
- id
- 036c6753-4c4a-46f5-84f6-5df5bb21f6a9
- date added to LUP
- 2021-02-22 13:22:28
- date last changed
- 2024-06-13 03:38:23
@article{036c6753-4c4a-46f5-84f6-5df5bb21f6a9,
abstract = {{<p>SUMMARY: Modern bioimaging and related areas such as sensor technology have undergone tremendous development over the last few years. As a result, contemporary imaging techniques, particularly electron microscopy (EM) and light sheet microscopy, can frequently generate datasets attaining sizes of several terabytes (TB). As a consequence, even seemingly simple data operations such as cropping, chromatic- and drift-corrections and even visualisation, poses challenges when applied to thousands of time points or tiles. To address this we developed BigDataProcessor2-a Fiji plugin facilitating processing workflows for TB sized image datasets.</p><p>AVAILABILITY AND IMPLEMENTATION: BigDataProcessor2 is available as a Fiji plugin via the BigDataProcessor update site. The application is implemented in Java and the code is publicly available on GitHub (https://github.com/bigdataprocessor/bigdataprocessor2).</p>}},
author = {{Tischer, Christian and Ravindran, Ashis and Reither, Sabine and Chiaruttini, Nicolas and Pepperkok, Rainer and Norlin, Nils}},
issn = {{1367-4803}},
language = {{eng}},
month = {{02}},
number = {{18}},
pages = {{3079--3081}},
publisher = {{Oxford University Press}},
series = {{Bioinformatics}},
title = {{BigDataProcessor2 : A free and open-source Fiji plugin for inspection and processing of TB sized image data}},
url = {{http://dx.doi.org/10.1093/bioinformatics/btab106}},
doi = {{10.1093/bioinformatics/btab106}},
volume = {{37}},
year = {{2021}},
}