Whole-brain PFC inputs (Le Merre and Ährlund-Richter, Neuron, 2021; methodology for Box 2)

The circular plot displays the number of discrete brain regions giving input (coral red) to the whole mouse PFC, the three PFC subdivisions and different isocortical regions, respectively. Dark blue: the proportion of the projections being reciprocal. The regions are plotted from the largest to the smallest number of input regions. The Venn diagram displays the number of unique and shared input regions for the three PFC subdivisions. Gray; input regions (n = 63) shared by all three PFC subdivisions. Each experiment in the Allen Institute for Brain Science connectome with an injection volume below 0.5 mm3 and a confirmed projection volume of 0.02mm3 (volumes of voxels labeled as projecting) in a target area was counted as an input region. Reciprocal connectivity was confirmed by the identification of a projection volume of 0.02mm3 in the input region from the target region.

PFC Functional Research Synthesis (Le Merre and Ährlund-Richter, Neuron, 2021; methodology for figure 3)

Data and methodology used to perform the functional research synthesis presented in the figure 3 of the perspective article: The mouse prefrontal cortex: Unity in diversity. The code used to generate the figures can be found on this github repository

3D visualisation

Here is an attempt of 3D visualisation of the database using plotly. Some improvements are still required. The Task type and Sensory Modality parameters are displayed as continuous variables although they are discrete variables. You can mouse over the dots in the scatter plot to see from which study is the data ONLY if you have already scrolled within the brain mesh (plotly feature). We hope to improve this 3D visualisation with time.


The database used to perform our research synthesis is available as a table. This table has the following columns: the year of the study, the short publication reference, the PFC region name used in the original publication, the inactivation method used, the stereotaxic triplet provided in the original article. The averaged coordinates used for the 3D plot into the Allen reference Atlas (ARA) CCFv3, the correction applied to the DV value to translate it into the ARA (see also below), the 3 scores; complexity index, sensory modality and task type, obtained for every publication, 7 logical values (in MOs, in ACA, in PL, in ILA, in ORBm, in ORBvl and in ORBl) indicating in which PFC region the study is found when plotted into the ARA CCFv3 with our method and the name of the Allen PFC region containing the stereotaxic triplet provided in the original publication.

The full database table can be downloaded here as an Excel or csv file.

YearRef ShortArea NameInactivation MethodAPMLDVDV originMean APMean MLMean DVCorrected DVBrain Surface DV CorrComplexity indexSensory ModalityTask typein MOsin ACAinPLin ILAin ORBmin ORBvlin ORBlAllen Atlas Annotation (2017)
2018Abbas et al., Neuron, 2018mPFCPhotoinhibition1,850,351,3DV brain surface1,850,351,32,0650,765463falsefalsetruefalsefalsefalsefalsePL
2017Allen et al., Neuron, 2017ALMPhotoinhibition, Muscimol2,420,5DV brain surface2,420,51,6851,185441truefalsefalsefalsefalsefalsefalseMOs
2018Allsop et al., Cell, 2018ACCPhtoinhibition10,32,1DV bregma10,32,12,1
2018Baltz et al., 2018OFCPhotoinhibition (PV-ChR2)/ Chemogenetics (hMD4)2,71,672,65DV Bregma2,71,672,652,650562truefalsefalsefalsefalsefalsefalseORBl
2020Bari et al., 2020dmPFCPhotoactivation (ChR2)1,70,32DV brain surface1,70,322,7450,745723falsefalsetruefalsefalsefalsefalsePL
2019Bari et al., Neuron 2019mPFCMuscimol (bilateral)2,50,51DV brain surface2,50,41,252,2951,045541falsefalsetruefalsefalsefalsefalsePL
2020Bariselli et al,. 2020OFCPhotoactivation (ChR2)2,51,12,5DV brain surface2,51,12,53,4150,915261falsefalsefalsefalsefalsefalsetrueORBvl
2017Barker et al., 2017IfL-CPhotoinhibition (arch)1,3-20,2-0,43DV Bregma1,650,3330362falsefalsefalsetruefalsefalsefalseILA
2015Beier et al., Cell, 2015mPFCPhotoactivation1,95-2,250,271,6-2,1DV brain surface2,10,271,852,8150,965662falsefalsefalsetruefalsefalsefalseILA
2019Berg et al., 2017ILPhotoactivation (Pyr- ChR2)1,660,31,6-2DV brain surface1,660,31,82,5350,735261falsefalsetruefalsefalsefalsefalsePL
2017Bolkan et al., Nat Neurosci, 2017mPFCPhtoinhibition1,750,41,8DV brain surface1,750,41,82,4850,685563falsefalsetruefalsefalsefalsefalsePL
2019Breton-Provencher and Sur, Nat Neurosci, 2019OFCPhotoactivation2,61,32DV bregma2,61,3220111falsefalsefalsefalsefalsefalsetrueORBl
2015Bukalo et al., Neuropsychology, 2015vmPFCPhotoinhibition1,80,32,8DV bregma1,80,32,82,80562falsefalsefalsetruefalsefalsefalseILA
2017Carus-Cadavieco et al., 2017mPFCPhotostimulation and inhibition (eNPAC2)1,70,352,7DV Bregma1,70,352,72,70261falsefalsetruefalsefalsefalsefalsePL
2019Cho et al., BioRxiv, 2019mPFCPhotoactivation1,70,32,75DV bregma1,70,32,752,750462falsefalsetruetruefalsefalsefalseILA
2015Cho et al., Neuron, 2015mPFCPhotoinhibition (arch)1,70,32,75DV bregma1,70,32,752,750462falsefalsetruetruefalsefalsefalseILA
2014Courtin et al., Nature, 2014dmPFCPhotoinhibition20,30,8-1,4DV brain surface20,31,11,9850,885612falsefalsetruefalsefalsefalsefalsePL
2016Dejean et al., 2016dmPFCPhotoinhibition (PV-ChR2)20,30,8-1,4DV brain surface20,31,22,0850,885513falsefalsetruefalsefalsefalsefalsePL
2020Esmaeili et al., 2020mPFCPhotoinhibition20,51,7DV brain surface20,51,72,4350,735561falsefalsetruefalsefalsefalsefalsePL
2016Felix-Ortiz et al., Neuroscience, 2016mPFCPhotostimulation1,70,31,9DV bregma1,70,31,91,90661falsefalsetruefalsefalsefalsefalsePL
2018Gilad et al., Neuron, 2018M2Photoinhibition1,50,50,5DV brain surface1,50,50,51,0350,535631truefalsefalsefalsefalsefalsefalseMOs
2016Goard et al., Elife, 2016fMCPhotoinhibition1,510,5DV brain surface1,510,50,9950,495621truefalsefalsefalsefalsefalsefalseMOs
2012Granon and Changeux, Behav Brain Res, 2012PLNMDA lesion1,9-2,80,3-0,41,5-2,5DV brain surface2,350,3523,0051,005463falsefalsefalsefalsetruefalsefalseORBm
2014Guo et al., Neuron, 2014ALMPhotoinhibition2,51,50,5DV brain surface2,51,50,51,5251,025731truefalsefalsefalsefalsefalsefalseMOs
2020Gutzeit et al., 2020IL-PFCPhotoactivation (ChR2)1,80,32,3DV Bregma1,80,32,32,30563falsefalsetruefalsefalsefalsefalsePL
2020Halladay et al., 2020vmPFCPhotoinhibition (Arch)1,5-2,50,52,7DV Bregma20,52,72,70563falsefalsetruetruefalsefalsefalseILA
2019Hare et al., 2019PL - ILPhotostimulation - DREADD (hM4D)1,90,42,5DV Bregma1,90,42,52,50361falsefalsetruefalsefalsefalsefalsePL
2020Heikenfeld et al., 2020mPFCPhotostimulation and inhibition (eNPAC2)1,50,33,1DV Bregma1,50,33,13,10463falsefalsefalsetruefalsefalsefalseILA
2019Hu et al., Neuron, 2019CgPhotoinhibition, Photoactivation0,30,31DV brain surface0,30,311,2350,235521falsetruefalsefalsefalsefalsefalseACA
2019Huang et al., 2019PLPhotoinhibition (NpHR) - Pharmacological ablation (dtA)1,90,52,1DV brain surface1,90,52,12,7950,695331falsefalsetruetruefalsefalsefalseILA
2018Huda et al., BioRxiv, 2018ACCPhotoinhibition0,50,50,5DV brain surface0,50,50,50,7050,205821truefalsefalsefalsefalsefalsefalseMOs
2018Inagaki et al., J.Neurosci, 2018ALMPhotoinhibition2,51,50,5DV brain surface2,51,50,51,5251,025611truefalsefalsefalsefalsefalsefalseMOs
2019Inagaki et al., Nature, 2019ALMPhotoinhibition2,51,50,5DV brain surface2,51,50,51,5251,025611truefalsefalsefalsefalsefalsefalseMOs
2018Itokazu et al., Nat Commun, 2018MOsPhotoinhibition0,70,70,25DV brain surface0,70,70,250,4950,245621truefalsefalsefalsefalsefalsefalseMOs
2019Jennings et al., Nature, 2019OFCPhotoactivation2,61,262,8DV bregma2,61,262,82,80461falsefalsefalsefalsefalsefalsetrueORBl
2018Jhang et al., 2018ACCPhotoactivation and inhibition (eNpHR3, ChR2)0,80,351,5DV Bregma0,80,351,51,50342falsetruefalsefalsefalsefalsefalseACA
2017Kamigaki and Dan, Nat Neurosci, 2017dmPFCPhotoinhibition1,8-2,10,3-0,40,8-1,2DV brain surface1,950,3511,8050,805411falsetruefalsefalsefalsefalsefalseACA
2016Kim et al., 2016ILPhotoactivation and inhibition (eNpHR3, ChR2)1,650,33,05DV Bregma1,650,33,053,050513falsefalsefalsetruefalsefalsefalseILA
2016Kim et al., Cell, 2016amPFCPhotoactivation1,90,41DV brain surface1,90,411,7550,755863falsetruefalsefalsefalsefalsefalseACA
2016Kim et al., Cell, 2016bmPFCPhotoactivation1,760,251,25DV brain surface1,760,251,252,0750,825823falsefalsetruefalsefalsefalsefalsePL
2017Kim et al., Cell, 2017mPFCPhotoinhibition2,10,352,2-2,3DV bregma2,10,352,252,250411falsefalsetruefalsefalsefalsefalsePL
2020Kingsbury et al., 2020dmPFCPhotoactivation (ChR2)20,31,8DV brain surface20,31,82,6850,885561falsefalsetruetruefalsefalsefalseILA
2017Klavir et al., Nat Neurosci, 2017mPFCPhotosactivation20,252,25DV bregma20,252,252,250512falsefalsetruefalsefalsefalsefalsePL
2016Koike et al., Neuropsychopharmacology, 2016dACCDREADD (hM4Di)1,7-1,1-0,40,2-0,2-0,40,7DV brain surface1,050,30,71,1950,4951023falsetruefalsefalsefalsefalsefalseACA
2013Kumar et al., 2013PrLPhotoactivation (ChR2, thy1-cre)2,650,250,8DV brain surface2,650,250,82,0851,285261falsefalsetruefalsefalsefalsefalsePL
2018Lak et al., BioRxiv, 2018PLVTA photoinhibition1,80,31,4DV brain surface1,80,31,42,1850,785721falsefalsetruefalsefalsefalsefalsePL
2018Le Merre et al., Neuron, 2018mPFCPhotoinhibition, Muscimol1,80,31,75DV brain surface1,80,31,752,5350,785231falsefalsetruefalsefalsefalsefalsePL
2019Lee et al., Neuron, 2019mPFCPhotoinhibition (arch)1,70,32,75DV bregma1,70,32,752,750261falsefalsetruetruefalsefalsefalseILA
2017Leinweber et al., Neuron, 2017A24bMuscimol10,30,5DV brain surface10,30,50,9750,475621truefalsefalsefalsefalsefalsefalseMOs
2020Li et al., 2020dmPFCPhotoactivation and inhibition (iC++, ChR2)10,50,8DV brain surface10,50,81,1650,365511truefalsefalsefalsefalsefalsefalseMOs
2015Li et al., Nature, 2015ALMPhotoinhibition2,51,50,5DV brain surface2,51,50,51,5251,025731truefalsefalsefalsefalsefalsefalseMOs
2016Li et al., Nature, 2016ALMPhotoinhibition2,51,50,5DV brain surface2,51,50,51,5251,025731truefalsefalsefalsefalsefalsefalseMOs
2016Liu et al., 2016ILSSFO1,750,452,8DV Bregma1,750,452,82,80462falsefalsetruetruefalsefalsefalseILA
2014Liu et al., Science, 2014mPFCPhotoinhibition, DREADD (hM4Di)1,960,421,62DV brain surface1,960,421,622,3850,765643falsefalsetruefalsefalsefalsefalsePL
2017Makino et al., Neuron, 2017M2Muscimol2,610,5DV brain surface2,610,51,4550,955411truefalsefalsefalsefalsefalsefalseMOs
2015Manita et al., Neuron, 2015M2Photoinhibition, TTX, CNQX2,190,630,5DV brain surface2,190,630,51,2750,775331truefalsefalsefalsefalsefalsefalseMOs
2015Manita et al., Neuron, 2015M2Photoinhibition, TTX, CNQX2,190,630,5DV brain surface2,190,630,51,2750,775531truefalsefalsefalsefalsefalsefalseMOs
2018Marton et al., J. of Neuro, 2018mPFCPhotoinhibition1,70,32,75DV bregma1,70,32,752,750462falsefalsetruetruefalsefalsefalseILA
2019Mayrhofer et al., Neuron, 2019ALMPhotoinhibition2,51,50,5DV brain surface2,51,50,51,5251,025361truefalsefalsefalsefalsefalsefalseMOs
2017Morandel et al., Scientific reports, 2017RFAPhotoinhibition2,70,90,5DV brain surface2,70,90,51,5051,005931truefalsefalsefalsefalsefalsefalseMOs
2012Morawska and Fendt, 2012mPFCMuscimol1,60,52,1DV brain surface1,60,52,12,6750,575513falsefalsetruefalsefalsefalsefalsePL
2017Murugan et al., Cell, 2017PLPhotoinhibition1,80,52,5DV bregma1,80,52,52,50663falsefalsetruefalsefalsefalsefalsePL
2019Nakajima et al., 2019PFCPhotoinhibition (eArch3)2,60,61DV brain surface2,60,611,9950,9951062falsefalsetruefalsefalsefalsefalsePL
2018Nakayama et al., 2018mPFCPhotoactivation and inhibition (Arch, ChR2)1,9-2,00,51,6DV brain surface1,950,51,62,3150,715462falsefalsetruefalsefalsefalsefalsePL
2019Namboodiri et al., 2019vmOFCPhotoinhibition (NpHR3)2,5-2,91-1,12,3DV brain surface2,71,052,33,3151,015411falsefalsefalsefalsefalsetruetrueORBvl
2019Newmyer et al., 2019ILPhotoactivation (ChR2, SSFO)1,80,41,8DV brain surface1,80,41,82,5050,705261falsefalsetruefalsefalsefalsefalsePL
2020Nguyen et al., 2020mPFCPhotoactivation and inhibition (Arch, ChR2)1,90,32,3DV Bregma1,90,32,32,30543falsefalsetruefalsefalsefalsefalsePL
2017Otis et al., Nature, 2017PFCPhotoinhibition, Photoactivation1,850,62,5DV bregma1,850,62,52,50411falsefalsetruefalsefalsefalsefalsePL
2019Padilla-Coreano et al., Neuron, 2019mPFCPhotoactivation1,60,41,25DV brain surface1,60,41,251,8850,635261falsetruetruefalsefalsefalsefalsePL
2018Pascoli et al., Nature, 2018OFCPhotoactivation2,61,61,8DV brain surface2,61,61,82,9051,105562falsefalsefalsefalsefalsefalsetrueORBl
2015Pinto and Dan, Neuron, 2015dmPFCMuscimol2,10,31,6DV brain surface2,10,31,62,5350,935511falsefalsetruefalsefalsefalsefalsePL
2019Pinto et al., Cell, 2019aM2Photoinhibition2,50,250,5DV brain surface2,50,250,51,7051,205621falsetruefalsefalsefalsefalsefalseACA
2019Pinto et al., Cell, 2019aM2Photoinhibition2,50,250,5DV brain surface2,50,250,51,7051,205721falsetruefalsefalsefalsefalsefalseACA
2016Popescu et al., PNAS, 2016mPFCPhotoactivation (DA)1,970,41,6-1,7DV brain surface1,970,41,652,4350,785211falsefalsetruefalsefalsefalsefalsePL
2015Rajasethupathy et al., 2015ACPhotoactivation and inhibition (eNpHR3, ChR2)10,31,2DV brain surface10,31,21,6750,475663falsetruefalsefalsefalsefalsefalseACA
2018Rikhye et al., Nat Neurosci, 2018PFCPhotoinhibition2,1-2,70,25-0,61,2-1,7 (ant) and 2-2,4 (post)DV brain surface2,40,431,832,8050,9751062falsefalsefalsefalsetruefalsefalseORBm
2018Rozeske et al., Neuron, 2018dmPFCPhotoinhibition1,980,351,5DV brain surface1,980,351,52,3250,825762falsefalsetruefalsefalsefalsefalsePL
2017Schmitt et al., Nature, 2017PFCPhotoinhibition, SSFO20,61,2-1,7 (ant) and 2-2,4 (post)DV brain surface20,61,832,5250,6951062falsefalsetruefalsefalsefalsefalsePL
2014Schneider et al., Nature, 2014M2Photoactivation10,50,5DV brain surface10,50,50,8650,365261truefalsefalsefalsefalsefalsefalseMOs
2020Sheggia et al., 2020mPFCPhotoactivation and inhibition (eNpHR3, ChR2)1,90,32,4DV Bregma1,90,32,42,40561falsefalsetruefalsefalsefalsefalsePL
2016Siniscalchi et al, Nat Neurosci, 2016M2Muscimol1,50,50.5DV brain surface1,50,50,51,0350,535712truefalsefalsefalsefalsefalsefalseMOs
2019Spellman et al., BioRxiv, 2019PFCMuscimol / Photoinhibition (stGtACR2)1,750,351,75DV brain surface1,750,351,752,4750,725762falsefalsetruefalsefalsefalsefalsePL
2015Spellman et al., Nature, 2015mPFCPhotoinhibition1,80,41,4DV brain surface1,80,41,42,1050,705413falsefalsetruefalsefalsefalsefalsePL
2018Starkweather et al., Neuron, 2018mPFCDREADD (KORD)2,70,250,6DV brain surface2,70,250,61,9251,325361falsefalsetruefalsefalsefalsefalsePL
2017Tamura et al., Nat Commun, 2017mPFCPhotoinhibition1,60,31,4DV brain surface1,60,31,42,1050,705443falsefalsetruefalsefalsefalsefalsePL
2019Tan et al., 2019PFCPhotoactivation (ChR2)2,250,451,2DV brain surface2,250,451,22,0750,875661falsefalsetruefalsefalsefalsefalsePL
2018Tuscher et al., 2018mPFCDREADD (hM4Di)1,80,32,7DV Bregma1,80,32,72,70561falsefalsetruefalsefalsefalsefalseILA
2013Van den Oever et al., 2013vmPFCPhotoactivation and inhibition (eNpHR3, ChR2)2,20,43DV Bregma2,20,4330563falsefalsefalsefalsetruefalsefalseORBm
2020Vertechi et al., 2020OFCPhotoinactivation (ChR2, Vgat)2,91,251,8DV brain surface2,91,251,82,9651,165361falsefalsefalsefalsefalsefalsetrueORBl
2018White et al., Cell Rep, 2018ACCPhotoinhibition0,74-1,340,31-1,25DV bregma1,040,31,131,1301063truefalsefalsefalsefalsefalsefalseMOs
2015Wimmer et al., Nature, 2015mPFCPhotoinhibition2,60,251,25DV brain surface2,60,251,252,5051,2551012falsefalsetruefalsetruefalsefalsePL
2020Wu et al., 2020ALMPhotoinhibition2,51,51,1DV Bregma2,51,51,11,10843truefalsefalsefalsefalsefalsefalseMOs
2019Xu et al., BioRxiv 2019ALMPhotoinhibition2,21,51,3DV brain surface2,21,51,32,1850,885331truefalsefalsefalsefalsefalsefalseMOs
2020Yamamuro et al., 2020mPFCPhotoactivation and inhibition (eNpHR3, ChR2), DREADD )hMD4)1,3-2,30,41-1,7DV brain surface1,80,41,352,0550,705661falsefalsetruefalsefalsefalsefalsePL
2016Ye et al., Cell, 2016mPFCPhotoactivation1,90,352,6DV bregma1,90,352,62,60261falsefalsetruefalsefalsefalsefalsePL
2011Yizhar et al., Nature, 2011mPFCSSFO1,80,352,0-2,85DV bregma1,80,352,432,430561falsefalsetruefalsefalsefalsefalsePL
2015Zhang et al., 2015PrLPhotoactivation and inhibition (Arch, ChR2)1,80,52,2DV Bregma1,80,52,22,20461falsefalsetruefalsefalsefalsefalsePL
2014Zhang et al., Science, 2014CgPhotoactivation0,20,30,9DV brain surface0,20,30,91,1050,205511falsetruefalsefalsefalsefalsefalseACA
2020Zhu et al., 2020PrLPhotoinhibition1,980,41,65DV brain surface1,980,41,652,4350,785643falsefalsetruefalsefalsefalsefalsePL
2017Zimmermann et al., Biol. Psychiatry, 2017OFCDREADD (BDNF KO)2,51,71,8DV bregma2,51,71,81,80462truefalsefalsefalsefalsefalsefalseMOs

Details on the sensory modality, task type and complexity index

The primary sensory modality utilized in the studies was simply reported as a score from 1 to 6; auditory (1), visual (2), somatosensory (3), olfactory (4), gustatory (5) or multisensory (combination of two or more modalities; 6), respectively. The task type in the studies was also reported with a score from 1 to 3; sensorimotor transformation (1), context/rule (2), or memory/delay (3), respectively. A complexity index (ranging from 1 to 10) was calculated for each study. The behavioral task in each study was scored according to eight criteria: number of stimuli, complexity of the stimuli (0, 1, or 2), number of actions to perform, complexity of the action to perform (0, 1, or 2), presence of a cue indicating the beginning of a trial (0 or 1), presence of a delay between task events (0 or 1), presence of a short- or long-term memory component (0 or 1), freely moving (1) or head-fixed (0) task.

The full table can be downloaded here as an Excel or csv file.

Ref ShortTaskNumber of StimuliComplexity of the StimuliNumber of ActionsComplexity of the ActionCueDelayMemory Component (long term)Freely Moving /HeadFixedFINAL SCORE
Abbas et al., Neuron, 2018spatial Working memory : delayed non-match-to-place task.0 (no)0 (no)2 (go right or left)0 (normal behavior)0 (no)1(10-60s)0 (no)14
Allen et al., Neuron, 2017olfactory go/no-go decision-making task 2 (odors)0 (pure odor)1 (licking)0 (normal behavior)1 (Sound)0 (no)0 (no)04
Allsop et al., Cell, 2018spatial Working memory : delayed non-match-to-place task.2 mouse being shocked in a context (fear cage)0 (pure)1 (freezing)0 (normal behavior)2 (compound light and 10kHz tone)0 (no)1 (24h)17
Baltz et al., 2018incentive learning task0 (no)0 (no)3 (2 lever press right-left, licking central port)1 (motor sequence)0 (no)0 (no)0 (no)15
Bari et al., 20202-choice task2 (lights)0 (flashing LED)2 (go right or left)0 (normal behavior)1 (reward port light at trial onset)1 (5s)0 (no)17
Bari et al., Neuron 2019dynamic foraging2 (odors)0 (pure odor)2 (lick right or left)0 (normal behavior)0 (no)0 (no)1 (previous trial)05
Bariselli et al,. 2020Open field on cocaine0 (no)0 (no)1 (exploration)0 (normal behavior)0 (no)0 (no)0 (no)12
Barker et al., 2017Contingency degradation0 (no)0 (no)1 (lever press, licking central port)1 (unatural)0 (no)0 (no)0 (no)13
Beier et al., Cell, 2015intracranial-self stimulation of mPFC->VTA projections0 (no)0 (no)5 ports0 (nose poking)0 (no)0 (no)0 (no)16
Berg et al., 2017Open field / Elevated plus maze0 (no)0 (no)1 (exploration)0 (normal behavior)0 (no)0 (no)0 (no)12
Bolkan et al., Nat Neurosci, 2017DNMTS T maze0 (no)0 (no)2 (go right or left)0 (normal behavior)0 (no)1(20-60s)0 (no)14
Breton-Provencher and Sur, Nat Neurosci, 2019Pupil dilatation1 (Sound)0 (pure tone)0 (nothing to do)0 (normal behavior)0 (no)0 (no)0 (no)01
Bukalo et al., Neuropsychology, 2015Contextual Fear conditioning2(fear cage, footshock)1 (full context)1 (freezing)0 (normal aversive behavior)0 (no)0 (no)1 (1day)15
Carus-Cadavieco et al., 2017Food rewarded learning task0 (no)0 (no)1 (nose poke, eating, drinking)0 (normal behavior)0 (no)0 (no)0 (no)12
Cho et al., BioRxiv, 2019attention set shifting task2 (olfactory and somatosensory)0 natural cues1 (dig reward)0 (normal behavior)0 (no)0 (no)0 (no)14
Cho et al., Neuron, 2015attention set shifting task2 (olfactory and somatosensory)0 natural cues1 (dig reward)0 (normal behavior)0 (no)0 (no)0 (no)14
Courtin et al., Nature, 2014Fear conditioning2 (sound, CS, footshock, US)0 (pure tone)1 (freezing)0 (normal behavior)0 (no)0 (no)1 (24h)16
Dejean et al., 2016Fear conditioning2 (sound, CS, footshock, US)0 (pure tone)1 (freezing)0 (normal behavior)0 (no)0 (no)1 (24h)15
Esmaeili et al., 2020delayed whisker detection task3 (visual,whisker,aud))0 (no)1 (licking)0 (normal behavior)0 (no)1 (1s)0 (no)05
Felix-Ortiz et al., Neuroscience, 2016social interaction1 juvenile mouse2(complex)1(social)1(Social behavior)0 (no)0 (no)0 (no)16
Gilad et al., Neuron, 2018Texture discrimination2 (textures)1 (more natural stimulus)1(lick)0 (normal behavior)1 (Sound)1(1,2-4,5s)0 (no)06
Goard et al., Elife, 2016Go/NoGo delayed visual task2 (visual gratings)1 (gratings)1(lick)0 (normal behavior)1 (sound)1 (0,3,6)0 (no)06
Granon and Changeux, Behav Brain Res, 2012Spatial learning and novel object and change of the baited arm (flexibility)0 (no)0 (no)2 (go right or left)0 (normal behavior)0 (no)0 (no)1(2min)14
Guo et al., Neuron, 2014whisker-based object localization task with a delayed, directional licking response2 (pole positions)1 (object localisation with whisker close or far)2 (lick rigth, lick left)0 (normal behavior)1 (Sound)1 (3s)0 (no)07
Gutzeit et al., 2020Contextual Fear conditioning2(fear cage, footshock)1 (full context)1 (freezing)0 (normal aversive behavior)0 (no)0 (no)1 (1day)15
Halladay et al., 2020Footshock punished EtOh self administration1 (footshock, US)0 (no)2 (lever press, licking central port)1 (unatural)0 (no)0 (no)0 (no)15
Hare et al., 2019Novelty supressed feeding0 (no)0 (no)1 (eating)0 (normal behavior)0 (no)0 (no)0 (no)12
Heikenfeld et al., 2020Spatial non match to sample0 (no)0 (no)2 (go right or left)0 (normal behavior)0 (no)1 (20s)0 (no)14
Hu et al., Neuron, 2019Go/No Go Visual discrimination task2 (visual gratings)1 (gratings)1(lick)0 (normal behavior)1 (Sound)0 (no)0 (no)05
Huang et al., 2019Paw withdrawal1 (nociceptive, paw)0 (no)1 (paw withdrawal)0 (normal behavior)0 (no)0 (no)0 (no)13
Huda et al., BioRxiv, 2018Visual forepaw orienting task2 (left - right)1 (square on a screen)2 (left right)1 (moving a trackball)1(sound)1 (500ms)0 (no)08
Inagaki et al., J.Neurosci, 2018Auditory delayed discrimination task2(sounds)0 (pure tone)2 (lick right or left)0 (normal behavior)1 (Sound)1(1,2s)0 (no)06
Inagaki et al., Nature, 2019Auditory delayed discrimination task2(sounds)0 (pure tone)2 (lick right or left)0 (normal behavior)1 (Sound)1(1,2s)0 (no)06
Itokazu et al., Nat Commun, 2018Sacade task in Mice !2 LEDs 0 (pure)2 (saccade forward or backward)1 (unatural inhead fixed)1 (fixation LED)0 (no)0 (no)06
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Bregma in CCFv3

The Allen Institute explicitly state that they do not have a definition for Bregma for the ~1600 adult mouse brains used to construct the CCFv3: “Each one of those brains was dissected from a skull, and every skull has a slightly different Bregma location; hence the CCF does not have a single brain-in-skull as a source (which would have a corresponding Bregma coordinate), but is made from brains out-of-skull that have been registered to achieve an ‘average’ volume that is defined by the brain itself, ex cranio. “ (source here). Therefore we had to place Bregma ourselves in the CCFv3. We placed Bregma based on the information available in the first version (CCFv1) of the ARA and how others labs have placed it (see the great Github repo of the Cortex lab from where we derived our scripts). Below, you can appreciate graphically where we place Bregma in the CCFv3. The matlab script “AllenCCFBregma.m” is carefully commented in regards to our coordinate triplet to provide transparency and reproducibility for other users.

DV Correction

Experimenters report the Bregma DV coordinate either relative to Brain surface or relative to Bregma 0 (skull landmark). In the Table1-Database we performed DV corrections to obtain the DV coordinate into the CCFv3. When Bregma was reported from the brain surface, we performed a correction with the matlab script “Bregma_DV_correction.mat”. This script plots the contours of the coronal section for the AP and ML coordinates provided in the referenced publication and finds the distance between brain the brain surface and the CCFv3 Bregma. This value needs to be added to the mean DV value provided in the original publication: column “Brain surface DV Corr” in Table1-Database. When Bregma was reported from Bregma 0 (skull landmark) no correction is needed.


The CCFv3 version of the Allen Atlas is a 10um voxel resolution space and our analysis using this Atlas has some limitations. We generated 3D meshes for the brain outline, for each PFC region (MOs, ACA, PL, ILA, ORBm, ORBvl and ORBl) and for the PFC sudivisions described in the section of our Perspective “Parcellations of the PFC” (dmPFC, vmPFC and vlPFC) by using the MATLAB “isosurface.m” function (see folder Brain_meshes). To detect in which Allen PFC region each publication was peformed we used the “inpolyhedron.m” function (Copyright © 2015, Sven Holcombe). The thickness of the borders in the actual version of the CCFv3 is around 30um (3 voxels). As a result some triplet of coordinates are allocated to 2 regions while performing our “inpolyhedron.m” detection procedure. We inspected manually each triplet of coordinates whithin its respective ARA plate (see folder AllenAtlasLocationCCFv3_individualstudies) and visually assesed for these ambiguous cases to which Allen PFC region they belong to. Our level of incertitude regarding PFC region assignment needs to be put into perspective because, as accurate as we can be as experimenters, the provided stereotaxic coordinates in every publication are only averaged values reflecting the mean location of the targetted brain structures. This experimental incertitude is by itself an important limitation of our analysis and needs to be taken into consideration.


© 2015 Allen Institute for Brain Science. Allen Mouse Brain Atlas (2015) with region annotations (2017).

A whole brain atlas of the monosynaptic input targeting four different cell-types in the medial prefrontal cortex of the mouse

The DMC Drive

Developed by Hoseok Kim, PhD, CarlenLab, Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden, Aug. 2019

General description

The DMC-drive is a small, light and simple positioning system for chronic electrophysiology experiments using multiple tetrodes in conjunction with optogenetics in mice and rats. The drive is composed of three parts that can be manufactured easily and at low cost using a CAD design file (Autodesk Inventor) and a 3D printer.

Download the files here.

The DMCdrive for chronic tetrode recordings with optogenetics


  1. Model name: DMC-drive
  2. Weight (without EIB): < 2g
  3. Size (L x W x H): 16 x 16 x 22mm
  4. Max. number of electrodes: 16 (4 tetrodes)
  5. Max. electrode travel distance: 4mm
  6. Screws & nut: M1.6-10mm hex socket cap head x1 (shuttle screw) / M1.6-thin hex nut x1 (shuttle nut) / M1-5mm slotted cheese head x2 (fixing screw for EIB, shuttle, and body part) / M1-2mm slotted cheese head x3 (fixing/anchor screw)
  7. Species: mouse or rat


  1. Shuttle (electrode carrier, holder)

2. Body

3. Case

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