DISCo: Deep learning, Instance Segmentation, and Correlations for cell segmentation in calcium imaging
Calcium imaging is one of the most important tools in neurophysiology as it enables the observation of neuronal activity for hundreds of cells in parallel and at single-cell resolution. In order to use the data gained with calcium imaging, it is necessary to extract individual cells and their activi...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article (Journal) Chapter/Article |
| Language: | English |
| Published: |
2019
|
| In: |
Arxiv
Year: 2019, Pages: 1-12 |
| DOI: | 10.48550/arXiv.1908.07957 |
| Online Access: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.48550/arXiv.1908.07957 Verlag, lizenzpflichtig, Volltext: http://arxiv.org/abs/1908.07957 
|
| Author Notes: | Elke Kirschbaum, Alberto Bailoni, Fred A. Hamprecht |
MARC
| LEADER | 00000caa a2200000 c 4500 | ||
|---|---|---|---|
| 001 | 1810083850 | ||
| 003 | DE-627 | ||
| 005 | 20220820222522.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 220713s2019 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.48550/arXiv.1908.07957 |2 doi | |
| 035 | |a (DE-627)1810083850 | ||
| 035 | |a (DE-599)KXP1810083850 | ||
| 035 | |a (OCoLC)1341463892 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rda | ||
| 041 | |a eng | ||
| 084 | |a 29 |2 sdnb | ||
| 100 | 1 | |a Kirschbaum, Elke |d 1990- |e VerfasserIn |0 (DE-588)1201608252 |0 (DE-627)1685675115 |4 aut | |
| 245 | 1 | 0 | |a DISCo |b Deep learning, Instance Segmentation, and Correlations for cell segmentation in calcium imaging |c Elke Kirschbaum, Alberto Bailoni, Fred A. Hamprecht |
| 264 | 1 | |c 2019 | |
| 300 | |a 12 | ||
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Identifizierung der Ressource nach: Last revised 4 Apr 2020 | ||
| 500 | |a Gesehen am 13.07.2022 | ||
| 520 | |a Calcium imaging is one of the most important tools in neurophysiology as it enables the observation of neuronal activity for hundreds of cells in parallel and at single-cell resolution. In order to use the data gained with calcium imaging, it is necessary to extract individual cells and their activity from the recordings. We present DISCo, a novel approach for the cell segmentation in calcium imaging videos. We use temporal information from the recordings in a computationally efficient way by computing correlations between pixels and combine it with shape-based information to identify active as well as non-active cells. We first learn to predict whether two pixels belong to the same cell; this information is summarized in an undirected, edge-weighted grid graph which we then partition. In so doing, we approximately solve the NP-hard correlation clustering problem with a recently proposed greedy algorithm. Evaluating our method on the Neurofinder public benchmark shows that DISCo outperforms all existing models trained on these datasets. | ||
| 650 | 4 | |a Computer Science - Machine Learning | |
| 650 | 4 | |a Electrical Engineering and Systems Science - Image and Video Processing | |
| 650 | 4 | |a Quantitative Biology - Neurons and Cognition | |
| 700 | 1 | |a Bailoni, Alberto |d 1992- |e VerfasserIn |0 (DE-588)1142007804 |0 (DE-627)1000981460 |0 (DE-576)494604050 |4 aut | |
| 700 | 1 | |a Hamprecht, Fred |e VerfasserIn |0 (DE-588)1020505605 |0 (DE-627)691240280 |0 (DE-576)360605516 |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Arxiv |d Ithaca, NY : Cornell University, 1991 |g (2019), Artikel-ID 1908.07957, Seite 1-12 |h Online-Ressource |w (DE-627)509006531 |w (DE-600)2225896-6 |w (DE-576)28130436X |7 nnas |a DISCo Deep learning, Instance Segmentation, and Correlations for cell segmentation in calcium imaging |
| 773 | 1 | 8 | |g year:2019 |g elocationid:1908.07957 |g pages:1-12 |g extent:12 |a DISCo Deep learning, Instance Segmentation, and Correlations for cell segmentation in calcium imaging |
| 856 | 4 | 0 | |u https://doi.org/10.48550/arXiv.1908.07957 |x Verlag |x Resolving-System |z lizenzpflichtig |3 Volltext |
| 856 | 4 | 0 | |u http://arxiv.org/abs/1908.07957 |x Verlag |z lizenzpflichtig |3 Volltext |
| 951 | |a AR | ||
| 992 | |a 20220713 | ||
| 993 | |a Article | ||
| 994 | |a 2019 | ||
| 998 | |g 1020505605 |a Hamprecht, Fred |m 1020505605:Hamprecht, Fred |d 700000 |d 708070 |d 700000 |d 728500 |e 700000PH1020505605 |e 708070PH1020505605 |e 700000PH1020505605 |e 728500PH1020505605 |k 0/700000/ |k 1/700000/708070/ |k 0/700000/ |k 1/700000/728500/ |p 3 |y j | ||
| 998 | |g 1142007804 |a Bailoni, Alberto |m 1142007804:Bailoni, Alberto |d 700000 |d 708000 |e 700000PB1142007804 |e 708000PB1142007804 |k 0/700000/ |k 1/700000/708000/ |p 2 | ||
| 998 | |g 1201608252 |a Kirschbaum, Elke |m 1201608252:Kirschbaum, Elke |d 700000 |d 708000 |e 700000PK1201608252 |e 708000PK1201608252 |k 0/700000/ |k 1/700000/708000/ |p 1 |x j | ||
| 999 | |a KXP-PPN1810083850 |e 4165090476 | ||
| BIB | |a Y | ||
| JSO | |a {"person":[{"family":"Kirschbaum","display":"Kirschbaum, Elke","role":"aut","given":"Elke"},{"given":"Alberto","role":"aut","family":"Bailoni","display":"Bailoni, Alberto"},{"display":"Hamprecht, Fred","family":"Hamprecht","given":"Fred","role":"aut"}],"title":[{"subtitle":"Deep learning, Instance Segmentation, and Correlations for cell segmentation in calcium imaging","title_sort":"DISCo","title":"DISCo"}],"note":["Identifizierung der Ressource nach: Last revised 4 Apr 2020","Gesehen am 13.07.2022"],"origin":[{"dateIssuedKey":"2019","dateIssuedDisp":"2019"}],"type":{"media":"Online-Ressource","bibl":"chapter"},"language":["eng"],"physDesc":[{"extent":"12 S."}],"name":{"displayForm":["Elke Kirschbaum, Alberto Bailoni, Fred A. Hamprecht"]},"recId":"1810083850","id":{"eki":["1810083850"],"doi":["10.48550/arXiv.1908.07957"]},"relHost":[{"disp":"DISCo Deep learning, Instance Segmentation, and Correlations for cell segmentation in calcium imagingArxiv","origin":[{"dateIssuedKey":"1991","publisher":"Cornell University ; Arxiv.org","publisherPlace":"Ithaca, NY ; [Erscheinungsort nicht ermittelbar]","dateIssuedDisp":"1991-"}],"note":["Gesehen am 28.05.2024"],"titleAlt":[{"title":"Arxiv.org"},{"title":"Arxiv.org e-print archive"},{"title":"Arxiv e-print archive"},{"title":"De.arxiv.org"}],"title":[{"title":"Arxiv","title_sort":"Arxiv"}],"type":{"media":"Online-Ressource","bibl":"edited-book"},"part":{"text":"(2019), Artikel-ID 1908.07957, Seite 1-12","pages":"1-12","year":"2019","extent":"12"},"language":["eng"],"physDesc":[{"extent":"Online-Ressource"}],"pubHistory":["1991 -"],"recId":"509006531","id":{"eki":["509006531"],"zdb":["2225896-6"]}}]} | ||
| SRT | |a KIRSCHBAUMDISCO2019 | ||