Back

CRASH2p: Closed-loop Two Photon Imaging in a Freely Moving Animal

McNulty, P.; Wu, R.; Yamaguchi, A.; Heckscher, E. H.; Haas, A.; Nwankpa, A.; Skanata, M. M.; Gershow, M. H.

2024-12-13 neuroscience
10.1101/2024.05.22.595209 bioRxiv
Show abstract

Direct measurement of neural activity in freely moving animals is essential for understanding how the brain controls and represents behaviors. Genetically encoded calcium indicators report neural activity as changes in fluorescence intensity, but brain motion confounds quantitative measurement of fluorescence. Translation, rotation, and deformation of the brain and the movements of intervening scattering or auto-fluorescent tissue all alter the amount of fluorescent light captured by a microscope. Compared to single-photon approaches, two photon microscopy is less sensitive to scattering and off-target fluorescence, but more sensitive to motion, and two photon imaging has always required anchoring the microscope to the brain. We developed a closed-loop resonant axial-scanning high-speed two photon (CRASH2p) microscope for real-time 3D motion correction in unrestrained animals, without implantation of reference markers. We complemented CRASH2p with a novel scanning strategy and a multi-stage registration pipeline. We performed volumetric ratiometrically corrected functional imaging in the CNS of freely moving Drosophila larvae and discovered previously unknown neural correlates of behavior.

Matching journals

The top 3 journals account for 50% of the predicted probability mass.

1
Nature Methods
○ 385 papers in training set
Top 0.3%
21.4%
Similar papers in this journal
2
eLife
● 5828 papers in training set
Top 4%
18.1%
Similar papers in this journal
3
Nature Communications
○ 5641 papers in training set
Top 16%
11.6%
Similar papers in this journal
50% of probability mass above
4
Current Biology
○ 665 papers in training set
Top 2%
6.6%
Similar papers in this journal
5
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 9%
5.4%
Similar papers in this journal
6
PLOS Biology
● 486 papers in training set
Top 1%
3.9%
7
Science Advances
● 1243 papers in training set
Top 13%
2.7%
8
PLOS Computational Biology
● 1863 papers in training set
Top 12%
2.3%
9
Science
● 477 papers in training set
Top 5%
1.9%
10
PLOS ONE
● 5266 papers in training set
Top 47%
1.7%
11
Scientific Reports
○ 3612 papers in training set
Top 54%
1.7%
12
Cell
○ 431 papers in training set
Top 6%
1.6%
13
eneuro
● 439 papers in training set
Top 5%
1.5%
14
Neuron
○ 337 papers in training set
Top 4%
1.5%
15
The Journal of Neuroscience
● 1025 papers in training set
Top 8%
1.5%
16
Cell Reports
○ 1498 papers in training set
Top 21%
1.5%
17
BMC Biology
○ 265 papers in training set
Top 3%
1.3%
18
Biomedical Optics Express
● 95 papers in training set
Top 0.7%
1.3%
19
Communications Biology
○ 993 papers in training set
Top 23%
1.1%
20
Cell Reports Methods
○ 165 papers in training set
Top 3%
1.0%
21
Development
● 497 papers in training set
Top 4%
1.0%
22
Optica
● 27 papers in training set
Top 0.3%
1.0%
23
Molecular Biology of the Cell
● 311 papers in training set
Top 3%
0.8%
24
iScience
○ 1154 papers in training set
Top 43%
0.6%
25
Nature Neuroscience
○ 252 papers in training set
Top 6%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.