The software is useful for any experiment requiring acquisition and generation of data and can be triggered in several modes.
During graduate school, I was making electrophysiological recordings and trying to synchronize various pieces of equipment (cameras, lasers, galvanometers, etc.). I found no software that was up to the task so I began a project to develop an uber-system capable of performing any data acquisition or generation operation that could be completed with the National Instruments DAQ hardware in use at the Yuste lab at the time. I jokingly referred to the project as “PackIO”, a combination of my name and IO, as in input/output, as the software is supposed to be able to take any input or generate any output in any synchronized fashion. The name stuck and now PackIO is in use by members of Rafael Yuste’s laboratory, Jason Maclean’s laboratory, Roberto Araya’s laboratory, and I continue to use PackIO in Michael Hausser’s laboratory.
Please read the Github wiki.
PackIO and EphysViewer are released under the GNU General Public License.
Most National Instruments DAQ cards should work. The following cards are known to work:
Watson BO, Yuste R, Packer AM (2016) PackIO and EphysViewer: software tools for acquisition and analysis of neuroscience data. bioRxiv http://dx.doi.org/10.1101/054080 Software available from www.packio.org.
Thank you to Rafael Yuste and all of the early beta testers in the Yuste lab. Mor Dar contributed some features to seal test and Carmen F. Fisac contributed the auto-incrementer available in version 273.
38: Zhang Z, Russell LE, Packer AM, Gauld OM, Häusser M (2018) Closed-loop all-optical interrogation of neural circuits in vivo Nature Methods LINK
37: Kwon T, Sakamoto M, Peterka DS, Yuste R (2017) Attenuation of Synaptic Potentials in Dendritic Spines. Cell Reports 20(5):1100-1110. LINK
36: Agetsuma M, Hamm JP, Tao K, Fujisawa S, Yuste R (2017) Parvalbumin-Positive Interneurons Regulate Neuronal Ensembles in Visual Cortex. Cerebral Cortex 1-15. LINK
35: Aitchison L, Russell L, Packer AM, Yan J, Castonguay P, Häusser M, Turaga SC (2017) Model-based Bayesian inference of neural activity and connectivity from all-optical interrogation of a neural circuit. Advances in Neural Information Processing Systems 3489-3498. LINK
34: Dupre D, Yuste R (2017) Non-overlapping Neural Networks in Hydra vulgaris. Current Biology 27:1085-1097. LINK
33: Jayant K, Hirtz JJ, Jen-La Plante I, Tsai DM, De Boer WDAM, Semonche A, Peterka DS, Owen JS, Sahin O, Shepard KL, Yuste R (2016) Targeted intracellular voltage recordings from dendritic spines using quantum-dot-coated nanopipettes. Nature Nanotechnology 12:335-342. LINK
32: Karnani MM, Jackson J, Ayzenshtat I, Tucciarone J, Manoocheri K, Snider WG, Yuste R (2016) Cooperative subnetworks of molecularly similar interneurons in mouse neocortex. Neuron 90:86-100. LINK
31: Karnani MM, Jackson J, Ayzenshtat I, Sichani AH, Manoocheri K, Kim S, Yuste R (2016) Opening holes in the blanket of inhibition: localized lateral disinhibition by VIP interneurons. J Neurosci 36(12):3471-3480. LINK
30: Packer AM, Russell LE, Dalgleish HWP, Häusser M (2015) Simultaneous all-optical targeted manipulation and recording of neural circuit activity with cellular resolution in vivo. Nature Methods 12:140-146. LINK
29: Sederberg AJ, Palmer SE, MacLean JN (2015) Decoding thalamic afferent input using microcircuit spiking activity. J Neurophysiol 113(7):2921-33. LINK
28: Runfeldt MJ, Sadovsky AJ, MacLean JN (2014) Acetylcholine functionally reorganizes neocortical microcircuits. J Neurophysiol 112(5):1205-16. LINK
27: Sadovsky AJ, MacLean JN (2014) Mouse visual neocortex supports multiple stereotyped patterns of microcircuit activity. J Neurosci 34(23):7769-77. LINK
26: Neubauer FB, Sederberg A, MacLean JN (2014) Local changes in neocortical circuit dynamics coincide with the spread of seizures to thalamus in a model of epilepsy. Front Neural Circuits 8:101. LINK
25: Araya R, Vogels TP, Yuste R (2014) Activity-dependent dendritic spine neck changes are correlated with synaptic strength. PNAS 111(28):E2895-904. LINK
24: Quirin, S, Jackson S, Peterka DS, Yuste R (2014) Simultaneous imaging of neural activity in three dimensions. Front Neural Circuits 8:29. LINK
23: Izquierdo-Serra M, Gascón-Moya M, Hirtz JJ, Pittolo S, Poskanzer KE, Ferrer È, Alibés R, Busqué F, Yuste R, Hernando J, Gorostiza P (2014) Two-photon neuronal and astrocytic stimulation with azobenzene-based photoswitches. J Am Chem Soc 136(24):8693-701. LINK
22: Araya R, Andino-Pavlovsky V, Yuste R, Etchenique R (2013) Two-photon optical interrogation of individual dendritic spines with caged dopamine. ACS Chem Neurosci. 4(8):1163-7. LINK
21: Sippy T, Yuste R (2013) Decorrelating action of inhibition in neocortical networks. J Neurosci. 33(23):9813-30. LINK
20: Packer AM, McConnell DJ, Fino E, Yuste R (2013) Axo-dendritic overlap and laminar projection can explain interneuron connectivity to pyramidal cells. Cerebral Cortex 23(12):2790-2802. *Selected for cover LINK
19: Sadovsky AJ, MacLean JN (2013) Scaling of topologically similar functional modules defines mouse primary auditory and somatosensory microcircuitry. J Neurosci. Aug 28;33(35):14048-60, 14060a. LINK
18: Kruskal PB, Li L, MacLean JN (2013) Circuit reactivation dynamically regulates synaptic plasticity in neocortex. Nat Commun 4:2574. LINK
17: Packer AM, Peterka DS, Hirtz JJ, Prakash R, Deisseroth K, Yuste R (2012) Two-photon optogenetics of dendritic spines and neural circuits. Nature Methods 9:1202-1205. LINK
16: Poskanzer KE, Yuste R (2011) Astrocytic regulation of cortical UP states. Proc Natl Acad Sci U S A. 108(45):18453-8. LINK
15: Woodruff AR, McGarry LM, Vogels TP, Inan M, Anderson SA, Yuste R (2011) State-dependent function of neocortical chandelier cells. J Neurosci. 2011 LINK
14: Fino E, Yuste R. (2011) Dense inhibitory connectivity in neocortex. Neuron 69(6):1188-203. LINK
13: Packer AM, Yuste R (2011) Dense, unspecific connectivity of neocortical parvalbumin-positive interneurons: a canonical microcircuit for inhibition? Journal of Neuroscience 31(37):13260-13271. *Selected for cover LINK
12: Ahmadian Y, Packer AM, Yuste R, Paninski L (2011) Designing optimal stimuli to control neuronal spike timing. J. Neurophys. 106(2):1038-1053. LINK
11: Sadovsky AJ, Kruskal PB, Kimmel JM, Ostmeyer J, Neubauer FB, MacLean JN (2011) Heuristically optimal path scanning for high-speed multiphoton circuit imaging. J Neurophysiol 106(3):1591-8. LINK
10: Watson BO, Nikolenko V, Araya R, Peterka DS, Woodruff A, Yuste R (2010) Two-photon microscopy with diffractive optical elements and spatial light modulators. Front Neurosci. 29. LINK
9: Vogelstein J, Packer AM, Machado T, Sippy T, Babadi B, Yuste R, Paninski L (2010) Fast non-negative deconvolution for spike train inference from population calcium imaging. J. Neurophys. 104(6):3691-704. LINK
8: McGarry LM, Packer AM, Fino E, Nikolenko V, Sippy T, Yuste R (2010) Quantitative classification of somatostatin-positive neocortical interneurons identifies three interneuron subtypes. Frontiers in Neural Circuits 4:12. LINK
7: Woodruff A, Xu Q, Anderson SA, Yuste R (2009) Depolarizing effect of neocortical chandelier neurons. Front Neural Circuits Oct 20;3:15. LINK
6: Vogelstein J, Watson B, Packer AM, Yuste R, Jedynak B, Paninski L (2009) Spike inference from calcium imaging using sequential Monte Carlo methods. Biophysical Journal 97:636-55. LINK
5: Watson BO, Nikolenko V, Yuste R (2009) Two-photon imaging with diffractive optical elements. Front Neural Circuits. 3:6. LINK
4: Fino E, Araya R, Peterka DS, Salierno M, Etchenique R, Yuste R (2009) RuBi-Glutamate: two-photon and visible-light photoactivation of neurons and dendritic spines. Front Neural Circuits 3(2). LINK
3: Nikolenko V, Watson BO, Araya R, Woodruff A, Peterka DS, Yuste R (2008) SLM microscopy: scanless two-photon imaging and photostimulation with spatial light modulators. Front Neural Circuits 2(5). LINK
2: Watson BO, Maclean JN, Yuste R (2008) UP States Protect Ongoing Cortical Activity from Thalamic Inputs. PLOS One 3(12). LINK
1: Nikolenko V, Poskanzer KE, Yuste R (2007) Two-photon photostimulation and imaging of neural circuits. Nature Methods 4(11) :943-950. LINK