update publication info [skip ci]

Author: kjohnsen

README.md

@@ -6,46 +6,46 @@
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![DOI](https://zenodo.org/badge/262130097.svg)](https://zenodo.org/doi/10.5281/zenodo.7036270)
 
-
 <h1>
 <p align="center">
-  <img 
-      style="display: block; 
+  <img
+      style="display: block;
              width: 50%;"
-      src="https://user-images.githubusercontent.com/19983357/187561700-100b853a-d226-4039-a580-1d798b00f9e4.png" 
+      src="https://user-images.githubusercontent.com/19983357/187561700-100b853a-d226-4039-a580-1d798b00f9e4.png"
       alt="Cleo: the Closed-Loop, Electrophysiology, and Optophysiology experiment simulation testbed">
   </img>
 </p>
 </h1>
 
-
 Hello there!
 Cleo has the goal of bridging theory and experiment for mesoscale neuroscience, facilitating electrode recording, optogenetic stimulation, and closed-loop experiments (e.g., real-time input and output processing) with the [Brian 2](https://brian2.readthedocs.io/en/stable/) spiking neural network simulator.
 We hope users will find these components useful for prototyping experiments, innovating methods, and testing observations about a hypotheses *in silico*, incorporating into spiking neural network models laboratory techniques ranging from passive observation to complex model-based feedback control.
 Cleo also serves as an extensible, modular base for developing additional recording and stimulation modules for Brian simulations.
 
 This package was developed by [Kyle Johnsen](https://kjohnsen.org) and Nathan Cruzado under the direction of [Chris Rozell](https://siplab.gatech.edu) at Georgia Institute of Technology.
-See the preprint [here](https://www.biorxiv.org/content/10.1101/2023.01.27.525963).
+See the publication [here](https://www.jneurosci.org/content/46/1/e2239242025).
 
 <p align="center">
-  <img 
-      style="display: block; 
+  <img
+      style="display: block;
              width: 90%;"
-      src="https://raw.githubusercontent.com/siplab-gt/cleo/master/docs/_static/cleo-overview-table.png" 
+      src="https://raw.githubusercontent.com/siplab-gt/cleo/master/docs/_static/cleo-overview-table.png"
       alt="Overview table of Cleo's closed-loop control, ephys, and ophys features">
   </img>
 </p>
 
 ## <img align="bottom" src="https://user-images.githubusercontent.com/19983357/167456512-fb10619b-255e-4a53-8ed9-79ae954d3ff4.png" alt="🖥️" > Closed Loop processing
+
 Cleo allows for flexible I/O processing in real time, enabling the simulation of closed-loop experiments such as event-triggered or feedback control.
 The user can also add latency to the stimulation to study the effects of computation delays.
 
-
 ## <img align="bottom" src="https://user-images.githubusercontent.com/19983357/167461111-b0a3746c-03fa-47b7-a9a9-7b651157044f.png" alt="🔌" > Electrode recording
+
 Cleo provides functions for configuring electrode arrays and placing them in arbitrary locations in the simulation.
 The user can then specify parameters for probabilistic spike detection or a spike-based LFP approximation developed by [Teleńczuk et al., 2020](https://www.sciencedirect.com/science/article/pii/S0165027020302946).
 
 ## <img align="bottom" src="https://user-images.githubusercontent.com/19983357/187728089-62fae854-1d69-4e8f-a597-a25934ca3eaa.png" alt="⚡" > 1P/2P optogenetic stimulation
+
 By modeling light propagation and opsins, Cleo enables users to flexibly add photostimulation to their model.
 Both a four-state Markov state model of opsin kinetics is available, as well as a minimal proportional current option for compatibility with simple neuron models.
 Cleo also accounts for opsin action spectra to model the effects of multi-light/wavelength/opsin crosstalk and heterogeneous expression.
@@ -57,14 +57,17 @@ Users can also inject a microscope into their model, selecting neurons on the sp
 The calcium indicator model of [Song et al., 2021](https://www.sciencedirect.com/science/article/pii/S0165027021001084) is implemented, with parameters included for GCaMP6 variants.
 
 ## 🚀 Getting started
+
 Just use pip to install&mdash;the name on PyPI is `cleosim`:
+
 ```bash
 pip install cleosim
 ```
 
 Then head to the [overview section of the documentation](https://cleosim.readthedocs.io/latest/overview.html) for a more detailed discussion of motivation, structure, and basic usage.
 
 ## 📚 Related resources
+
 Those using Cleo to simulate closed-loop control experiments may be interested in software developed for the execution of real-time, *in-vivo* experiments.
 Developed by members of [Chris Rozell](https://siplab.gatech.edu)'s and [Garrett Stanley](https://stanley.gatech.edu/)'s labs at Georgia Tech, the [CLOCTools repository](https://cloctools.github.io) can serve these users in two ways:
 
@@ -74,23 +77,25 @@ Although Cleo enables closed-loop manipulation of network simulations, it does n
 The `ldsCtrlEst` library implements adaptive linear dynamical system-based control while the `hmm` library can generate and decode systems with discrete latent states and observations.
 
 <p align="center">
-  <img 
-      style="display: block; 
+  <img
+      style="display: block;
              width: 100%;"
-      src="https://raw.githubusercontent.com/siplab-gt/cleo/master/docs/_static/cloctools_and_cleo.png" 
+      src="https://raw.githubusercontent.com/siplab-gt/cleo/master/docs/_static/cloctools_and_cleo.png"
       alt="CLOCTools and Cleo">
   </img>
 </p>
 
 ### 📃 Publications
-[**Cleo: A testbed for bridging model and experiment by simulating closed-loop stimulation, electrode recording, and optophysiology**](https://www.biorxiv.org/content/10.1101/2023.01.27.525963)<br>
-K.A. Johnsen, N.A. Cruzado, Z.C. Menard, A.A. Willats, A.S. Charles, and C.J. Rozell. *bioRxiv*, 2023.
 
-[**CLOC Tools: A Library of Tools for Closed-Loop Neuroscience**](https://github.com/cloctools/tools-for-neuro-control-manuscript)<br>
+[**Bridging Model and Experiment in Systems Neuroscience with Cleo: The Closed-Loop, Electrophysiology, and Optophysiology Simulation Testbed**](https://www.jneurosci.org/content/46/1/e2239242025)<br>
+K.A. Johnsen, N.A. Cruzado, Z.C. Menard, A.A. Willats, A.S. Charles, J.E. Markowitz, and C.J. Rozell. *Journal of Neuroscience*, 2026.
+
+<!-- THESE AREN'T PUBLICLY VIEWABLE -->
+<!-- [**CLOC Tools: A Library of Tools for Closed-Loop Neuroscience**](https://github.com/cloctools/tools-for-neuro-control-manuscript)<br>
 A.A. Willats, M.F. Bolus, K.A. Johnsen, G.B. Stanley, and C.J. Rozell. *In prep*, 2023.
 
 [**State-Aware Control of Switching Neural Dynamics**](https://github.com/awillats/state-aware-control)<br>
-A.A. Willats, M.F. Bolus, C.J. Whitmire, G.B. Stanley, and C.J. Rozell. *In prep*, 2023.
+A.A. Willats, M.F. Bolus, C.J. Whitmire, G.B. Stanley, and C.J. Rozell. *In prep*, 2023. -->
 
 [**Closed-Loop Identifiability in Neural Circuits**](https://github.com/awillats/clinc)<br>
 A. Willats, M. O'Shaughnessy, and C. Rozell. *In prep*, 2023.

docs/showcase.md

@@ -2,9 +2,9 @@
 
 Here you can find links to code where Cleo has been used in research.
 
-- Cleo [preprint](https://www.biorxiv.org/content/10.1101/2023.01.27.525963)
-    - [Seizure recording and SWR evocation experiments in a hippocampus model](https://github.com/siplab-gt/cleo-hpc-experiments)
-    - [Bidirectional in-vitro "optoclamp" of firing rate](https://github.com/siplab-gt/cleo/blob/master/notebooks/newman15_validation.ipynb)
-    - [All-optical control of individual neurons with off-target effects](https://github.com/siplab-gt/cleo/blob/master/notebooks/all_optical_fig.ipynb)
-    - [Closed-loop rejection of a traveling wave in rodent S1](https://github.com/siplab-gt/cleo-traveling-wave-rejection)
-    - [Firing rate clamp to disrupt mouse V1 plasticity](https://github.com/siplab-gt/cleo-v1-plasticity-expt)
+- Cleo [publication](https://www.jneurosci.org/content/46/1/e2239242025)
+  - [Seizure recording and SWR evocation experiments in a hippocampus model](https://github.com/siplab-gt/cleo-hpc-experiments)
+  - [Bidirectional in-vitro "optoclamp" of firing rate](https://github.com/siplab-gt/cleo/blob/master/notebooks/newman15_validation.ipynb)
+  - [All-optical control of individual neurons with off-target effects](https://github.com/siplab-gt/cleo/blob/master/notebooks/all_optical_fig.ipynb)
+  - [Closed-loop rejection of a traveling wave in rodent S1](https://github.com/siplab-gt/cleo-traveling-wave-rejection)
+  - [Firing rate clamp to disrupt mouse V1 plasticity](https://github.com/siplab-gt/cleo-v1-plasticity-expt)