diff --git a/src/eigenvalue.cpp b/src/eigenvalue.cpp
index d0e4936088..ccf70ee2ea 100644
--- a/src/eigenvalue.cpp
+++ b/src/eigenvalue.cpp
@@ -608,8 +608,7 @@ double ufs_get_weight(const Particle* p)
   auto& m = model::meshes[settings::index_ufs_mesh];
 
   // Determine indices on ufs mesh for current location
-  // TODO: off by one
-  int mesh_bin = m->get_bin({p->coord[0].xyz}) - 1;
+  int mesh_bin = m->get_bin({p->coord[0].xyz});
   if (mesh_bin < 0) {
     p->write_restart();
     fatal_error("Source site outside UFS mesh!");
diff --git a/src/mesh.cpp b/src/mesh.cpp
index b02a49ff4b..ab263cd77c 100644
--- a/src/mesh.cpp
+++ b/src/mesh.cpp
@@ -168,11 +168,11 @@ int RegularMesh::get_bin_from_indices(const int* ijk) const
 {
   switch (n_dimension_) {
     case 1:
-      return ijk[0];
+      return ijk[0] - 1;
     case 2:
-      return (ijk[1] - 1)*shape_[0] + ijk[0];
+      return (ijk[1] - 1)*shape_[0] + ijk[0] - 1;
     case 3:
-      return ((ijk[2] - 1)*shape_[1] + (ijk[1] - 1))*shape_[0] + ijk[0];
+      return ((ijk[2] - 1)*shape_[1] + (ijk[1] - 1))*shape_[0] + ijk[0] - 1;
     default:
       throw std::runtime_error{"Invalid number of mesh dimensions"};
   }
@@ -193,14 +193,14 @@ void RegularMesh::get_indices(Position r, int* ijk, bool* in_mesh) const
 void RegularMesh::get_indices_from_bin(int bin, int* ijk) const
 {
   if (n_dimension_ == 1) {
-    ijk[0] = bin;
+    ijk[0] = bin + 1;
   } else if (n_dimension_ == 2) {
-    ijk[0] = (bin - 1) % shape_[0] + 1;
-    ijk[1] = (bin - 1) / shape_[0] + 1;
+    ijk[0] = bin % shape_[0] + 1;
+    ijk[1] = bin / shape_[0] + 1;
   } else if (n_dimension_ == 3) {
-    ijk[0] = (bin - 1) % shape_[0] + 1;
-    ijk[1] = ((bin - 1) % (shape_[0] * shape_[1])) / shape_[0] + 1;
-    ijk[2] = (bin - 1) / (shape_[0] * shape_[1]) + 1;
+    ijk[0] = bin % shape_[0] + 1;
+    ijk[1] = (bin % (shape_[0] * shape_[1])) / shape_[0] + 1;
+    ijk[2] = bin / (shape_[0] * shape_[1]) + 1;
   }
 }
 
@@ -586,7 +586,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p, std::vector<int>& bins
           if (xt::all(ijk0 >= 1) && xt::all(ijk0 <= shape_)) {
             int i_surf = 4*i + 3;
             int i_mesh = get_bin_from_indices(ijk0.data());
-            int i_bin = 4*n*(i_mesh - 1) + i_surf;
+            int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
           }
@@ -600,7 +600,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p, std::vector<int>& bins
           if (xt::all(ijk0 >= 1) && xt::all(ijk0 <= shape_)) {
             int i_surf = 4*i + 2;
             int i_mesh = get_bin_from_indices(ijk0.data());
-            int i_bin = 4*n*(i_mesh - 1) + i_surf;
+            int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
           }
@@ -612,7 +612,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p, std::vector<int>& bins
           if (xt::all(ijk0 >= 1) && xt::all(ijk0 <= shape_) ){
             int i_surf = 4*i + 1;
             int i_mesh = get_bin_from_indices(ijk0.data());
-            int i_bin = 4*n*(i_mesh - 1) + i_surf;
+            int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
           }
@@ -626,7 +626,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p, std::vector<int>& bins
           if (xt::all(ijk0 >= 1) && xt::all(ijk0 <= shape_)) {
             int i_surf = 4*i + 4;
             int i_mesh = get_bin_from_indices(ijk0.data());
-            int i_bin = 4*n*(i_mesh - 1) + i_surf;
+            int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
           }
@@ -670,8 +670,7 @@ xt::xarray<double> RegularMesh::count_sites(int64_t n, const Bank* bank,
 
   for (int64_t i = 0; i < n; ++i) {
     // determine scoring bin for entropy mesh
-    // TODO: off-by-one
-    int mesh_bin = get_bin({bank[i].xyz}) - 1;
+    int mesh_bin = get_bin({bank[i].xyz});
 
     // if outside mesh, skip particle
     if (mesh_bin < 0) {
diff --git a/src/output.cpp b/src/output.cpp
index 97436dc244..095a175269 100644
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -679,13 +679,12 @@ write_tallies()
       // prevents redundant output.
       int indent = 0;
       for (auto i = 0; i < tally.filters().size(); ++i) {
-        if ((filter_index-1) % tally.strides(i) == 0) {
+        if (filter_index % tally.strides(i) == 0) {
           auto i_filt = tally.filters(i);
           const auto& filt {*model::tally_filters[i_filt]};
           auto& match {simulation::filter_matches[i_filt]};
           tallies_out << std::string(indent+1, ' ')
-            // TODO: off-by-one
-            << filt.text_label(match.i_bin_+1) << "\n";
+            << filt.text_label(match.i_bin_) << "\n";
         }
         indent += 2;
       }
@@ -712,9 +711,8 @@ write_tallies()
           std::string score_name = score > 0 ? reaction_name(score)
             : score_names.at(score);
           double mean, stdev;
-          //TODO: off-by-one
           std::tie(mean, stdev) = mean_stdev(
-            &tally.results_(filter_index-1, score_index, 0), tally.n_realizations_);
+            &tally.results_(filter_index, score_index, 0), tally.n_realizations_);
           tallies_out << std::string(indent+1, ' ')  << std::left
             << std::setw(36) << score_name << " " << mean << " +/- "
             << t_value * stdev << "\n";
diff --git a/src/physics.cpp b/src/physics.cpp
index 23ce8f5603..5d6ca2dee7 100644
--- a/src/physics.cpp
+++ b/src/physics.cpp
@@ -670,7 +670,6 @@ void scatter(Particle* p, int i_nuclide)
   p->event = EVENT_SCATTER;
 
   // Sample new outgoing angle for isotropic-in-lab scattering
-  // TODO: off-by-one
   const auto& mat {model::materials[p->material]};
   if (!mat->p0_.empty()) {
     int i_nuc_mat = mat->mat_nuclide_index_[i_nuclide];
diff --git a/src/state_point.cpp b/src/state_point.cpp
index 3730c32163..cca622950c 100644
--- a/src/state_point.cpp
+++ b/src/state_point.cpp
@@ -123,7 +123,6 @@ openmc_statepoint_write(const char* filename, bool* write_source)
           write_dataset(deriv_group, "independent variable", "density");
         } else if (deriv.variable == DIFF_NUCLIDE_DENSITY) {
           write_dataset(deriv_group, "independent variable", "nuclide_density");
-          //TODO: off-by-one
           write_dataset(deriv_group, "nuclide",
             data::nuclides[deriv.diff_nuclide]->name_);
         } else if (deriv.variable == DIFF_TEMPERATURE) {
diff --git a/src/tallies/derivative.cpp b/src/tallies/derivative.cpp
index 1098adc550..2ad251b736 100644
--- a/src/tallies/derivative.cpp
+++ b/src/tallies/derivative.cpp
@@ -656,7 +656,6 @@ void score_collision_derivative(const Particle* p)
       // Loop over the material's nuclides until we find the event nuclide.
       for (auto i_nuc : material.nuclide_) {
         const auto& nuc {*data::nuclides[i_nuc]};
-        //TODO: off-by-one
         if (i_nuc == p->event_nuclide && multipole_in_range(&nuc, p->last_E)) {
           // phi is proportional to Sigma_s
           // (1 / phi) * (d_phi / d_T) = (d_Sigma_s / d_T) / Sigma_s
diff --git a/src/tallies/filter_azimuthal.cpp b/src/tallies/filter_azimuthal.cpp
index dc65284820..f4e265dd81 100644
--- a/src/tallies/filter_azimuthal.cpp
+++ b/src/tallies/filter_azimuthal.cpp
@@ -48,8 +48,7 @@ AzimuthalFilter::get_all_bins(const Particle* p, int estimator,
   }
 
   if (phi >= bins_.front() && phi <= bins_.back()) {
-    //TODO: off-by-one
-    auto bin = lower_bound_index(bins_.begin(), bins_.end(), phi) + 1;
+    auto bin = lower_bound_index(bins_.begin(), bins_.end(), phi);
     match.bins_.push_back(bin);
     match.weights_.push_back(1.0);
   }
@@ -66,8 +65,7 @@ std::string
 AzimuthalFilter::text_label(int bin) const
 {
   std::stringstream out;
-  //TODO: off-by-one
-  out << "Azimuthal Angle [" << bins_[bin-1] << ", " << bins_[bin] << ")";
+  out << "Azimuthal Angle [" << bins_[bin] << ", " << bins_[bin+1] << ")";
   return out.str();
 }
 
diff --git a/src/tallies/filter_cell.cpp b/src/tallies/filter_cell.cpp
index 4e25e8541b..1b2b054169 100644
--- a/src/tallies/filter_cell.cpp
+++ b/src/tallies/filter_cell.cpp
@@ -44,8 +44,7 @@ CellFilter::get_all_bins(const Particle* p, int estimator,
   for (int i = 0; i < p->n_coord; i++) {
     auto search = map_.find(p->coord[i].cell);
     if (search != map_.end()) {
-      //TODO: off-by-one
-      match.bins_.push_back(search->second + 1);
+      match.bins_.push_back(search->second);
       match.weights_.push_back(1.0);
     }
   }
@@ -63,8 +62,7 @@ CellFilter::to_statepoint(hid_t filter_group) const
 std::string
 CellFilter::text_label(int bin) const
 {
-  //TODO: off-by-one
-  return "Cell " + std::to_string(model::cells[cells_[bin-1]]->id_);
+  return "Cell " + std::to_string(model::cells[cells_[bin]]->id_);
 }
 
 //==============================================================================
diff --git a/src/tallies/filter_cellborn.cpp b/src/tallies/filter_cellborn.cpp
index b173b2e393..005d3844bf 100644
--- a/src/tallies/filter_cellborn.cpp
+++ b/src/tallies/filter_cellborn.cpp
@@ -10,8 +10,7 @@ CellbornFilter::get_all_bins(const Particle* p, int estimator,
 {
   auto search = map_.find(p->cell_born);
   if (search != map_.end()) {
-    //TODO: off-by-one
-    match.bins_.push_back(search->second + 1);
+    match.bins_.push_back(search->second);
     match.weights_.push_back(1.0);
   }
 }
@@ -19,8 +18,7 @@ CellbornFilter::get_all_bins(const Particle* p, int estimator,
 std::string
 CellbornFilter::text_label(int bin) const
 {
-  //TODO: off-by-one
-  return "Birth Cell " + std::to_string(model::cells[cells_[bin-1]]->id_);
+  return "Birth Cell " + std::to_string(model::cells[cells_[bin]]->id_);
 }
 
 } // namespace openmc
diff --git a/src/tallies/filter_cellfrom.cpp b/src/tallies/filter_cellfrom.cpp
index 1262ebecd3..9a43f7c431 100644
--- a/src/tallies/filter_cellfrom.cpp
+++ b/src/tallies/filter_cellfrom.cpp
@@ -11,8 +11,7 @@ CellFromFilter::get_all_bins(const Particle* p, int estimator,
   for (int i = 0; i < p->last_n_coord; i++) {
     auto search = map_.find(p->last_cell[i]);
     if (search != map_.end()) {
-      //TODO: off-by-one
-      match.bins_.push_back(search->second + 1);
+      match.bins_.push_back(search->second);
       match.weights_.push_back(1.0);
     }
   }
@@ -21,8 +20,7 @@ CellFromFilter::get_all_bins(const Particle* p, int estimator,
 std::string
 CellFromFilter::text_label(int bin) const
 {
-  //TODO: off-by-one
-  return "Cell from " + std::to_string(model::cells[cells_[bin-1]]->id_);
+  return "Cell from " + std::to_string(model::cells[cells_[bin]]->id_);
 }
 
 } // namespace openmc
diff --git a/src/tallies/filter_delayedgroup.cpp b/src/tallies/filter_delayedgroup.cpp
index f1876fae9c..4f448358e3 100644
--- a/src/tallies/filter_delayedgroup.cpp
+++ b/src/tallies/filter_delayedgroup.cpp
@@ -29,8 +29,7 @@ void
 DelayedGroupFilter::get_all_bins(const Particle* p, int estimator,
                                  FilterMatch& match) const
 {
-  //TODO: off-by-one
-  match.bins_.push_back(1);
+  match.bins_.push_back(0);
   match.weights_.push_back(1.0);
 }
 
@@ -44,8 +43,7 @@ DelayedGroupFilter::to_statepoint(hid_t filter_group) const
 std::string
 DelayedGroupFilter::text_label(int bin) const
 {
-  //TODO: off-by-one
-  return "Delayed Group " + std::to_string(groups_[bin-1]);
+  return "Delayed Group " + std::to_string(groups_[bin]);
 }
 
 } // namespace openmc
diff --git a/src/tallies/filter_distribcell.cpp b/src/tallies/filter_distribcell.cpp
index ee4f08dd44..ab7ea67cf2 100644
--- a/src/tallies/filter_distribcell.cpp
+++ b/src/tallies/filter_distribcell.cpp
@@ -54,8 +54,7 @@ DistribcellFilter::get_all_bins(const Particle* p, int estimator,
       }
     }
     if (cell_ == p->coord[i].cell) {
-      //TODO: off-by-one
-      match.bins_.push_back(offset + 1);
+      match.bins_.push_back(offset);
       match.weights_.push_back(1.0);
       return;
     }
@@ -73,8 +72,7 @@ std::string
 DistribcellFilter::text_label(int bin) const
 {
   auto map = model::cells[cell_]->distribcell_index_;
-  //TODO: off-by-one
-  auto path = distribcell_path(cell_, map, bin-1);
+  auto path = distribcell_path(cell_, map, bin);
   return "Distributed Cell " + path;
 }
 
diff --git a/src/tallies/filter_energy.cpp b/src/tallies/filter_energy.cpp
index 90cd7b3bfe..4cbde1cc45 100644
--- a/src/tallies/filter_energy.cpp
+++ b/src/tallies/filter_energy.cpp
@@ -43,11 +43,9 @@ const
 {
   if (p->g != F90_NONE && matches_transport_groups_) {
     if (estimator == ESTIMATOR_TRACKLENGTH) {
-      //TODO: off-by-one
-      match.bins_.push_back(data::num_energy_groups - p->g + 1);
+      match.bins_.push_back(data::num_energy_groups - p->g);
     } else {
-      //TODO: off-by-one
-      match.bins_.push_back(data::num_energy_groups - p->last_g + 1);
+      match.bins_.push_back(data::num_energy_groups - p->last_g);
     }
     match.weights_.push_back(1.0);
 
@@ -57,8 +55,7 @@ const
 
     // Bin the energy.
     if (E >= bins_.front() && E <= bins_.back()) {
-      //TODO: off-by-one
-      auto bin = lower_bound_index(bins_.begin(), bins_.end(), E) + 1;
+      auto bin = lower_bound_index(bins_.begin(), bins_.end(), E);
       match.bins_.push_back(bin);
       match.weights_.push_back(1.0);
     }
@@ -76,8 +73,7 @@ std::string
 EnergyFilter::text_label(int bin) const
 {
   std::stringstream out;
-  //TODO: off-by-one
-  out << "Incoming Energy [" << bins_[bin-1] << ", " << bins_[bin] << ")";
+  out << "Incoming Energy [" << bins_[bin] << ", " << bins_[bin+1] << ")";
   return out.str();
 }
 
@@ -90,13 +86,12 @@ EnergyoutFilter::get_all_bins(const Particle* p, int estimator,
                               FilterMatch& match) const
 {
   if (p->g != F90_NONE && matches_transport_groups_) {
-    match.bins_.push_back(data::num_energy_groups - p->g + 1);
+    match.bins_.push_back(data::num_energy_groups - p->g);
     match.weights_.push_back(1.0);
 
   } else {
     if (p->E >= bins_.front() && p->E <= bins_.back()) {
-      //TODO: off-by-one
-      auto bin = lower_bound_index(bins_.begin(), bins_.end(), p->E) + 1;
+      auto bin = lower_bound_index(bins_.begin(), bins_.end(), p->E);
       match.bins_.push_back(bin);
       match.weights_.push_back(1.0);
     }
@@ -107,8 +102,7 @@ std::string
 EnergyoutFilter::text_label(int bin) const
 {
   std::stringstream out;
-  //TODO: off-by-one
-  out << "Outgoing Energy [" << bins_[bin-1] << ", " << bins_[bin] << ")";
+  out << "Outgoing Energy [" << bins_[bin] << ", " << bins_[bin+1] << ")";
   return out.str();
 }
 
diff --git a/src/tallies/filter_energyfunc.cpp b/src/tallies/filter_energyfunc.cpp
index b47e7b7b63..3c616aabfc 100644
--- a/src/tallies/filter_energyfunc.cpp
+++ b/src/tallies/filter_energyfunc.cpp
@@ -41,8 +41,7 @@ EnergyFunctionFilter::get_all_bins(const Particle* p, int estimator,
     double f = (p->last_E - energy_[i]) / (energy_[i+1] - energy_[i]);
 
     // Interpolate on the lin-lin grid.
-    //TODO: off-by-one
-    match.bins_.push_back(1);
+    match.bins_.push_back(0);
     match.weights_.push_back((1-f) * y_[i] + f * y_[i+1]);
   }
 }
diff --git a/src/tallies/filter_legendre.cpp b/src/tallies/filter_legendre.cpp
index a5f583a158..1e799932ad 100644
--- a/src/tallies/filter_legendre.cpp
+++ b/src/tallies/filter_legendre.cpp
@@ -21,8 +21,7 @@ LegendreFilter::get_all_bins(const Particle* p, int estimator,
   double wgt[n_bins_];
   calc_pn_c(order_, p->mu, wgt);
   for (int i = 0; i < n_bins_; i++) {
-    //TODO: off-by-one
-    match.bins_.push_back(i + 1);
+    match.bins_.push_back(i);
     match.weights_.push_back(wgt[i]);
   }
 }
@@ -37,8 +36,7 @@ LegendreFilter::to_statepoint(hid_t filter_group) const
 std::string
 LegendreFilter::text_label(int bin) const
 {
-  //TODO: off-by-one
-  return "Legendre expansion, P" + std::to_string(bin - 1);
+  return "Legendre expansion, P" + std::to_string(bin);
 }
 
 //==============================================================================
diff --git a/src/tallies/filter_material.cpp b/src/tallies/filter_material.cpp
index 488f962fa7..a4da2deb17 100644
--- a/src/tallies/filter_material.cpp
+++ b/src/tallies/filter_material.cpp
@@ -44,8 +44,7 @@ MaterialFilter::get_all_bins(const Particle* p, int estimator,
 {
   auto search = map_.find(p->material);
   if (search != map_.end()) {
-    //TODO: off-by-one
-    match.bins_.push_back(search->second + 1);
+    match.bins_.push_back(search->second);
     match.weights_.push_back(1.0);
   }
 }
@@ -62,8 +61,7 @@ MaterialFilter::to_statepoint(hid_t filter_group) const
 std::string
 MaterialFilter::text_label(int bin) const
 {
-  //TODO: off-by-one
-  return "Material " + std::to_string(model::materials[materials_[bin-1]]->id_);
+  return "Material " + std::to_string(model::materials[materials_[bin]]->id_);
 }
 
 //==============================================================================
diff --git a/src/tallies/filter_mesh.cpp b/src/tallies/filter_mesh.cpp
index 324e38cc7b..177dc407e4 100644
--- a/src/tallies/filter_mesh.cpp
+++ b/src/tallies/filter_mesh.cpp
@@ -25,7 +25,7 @@ MeshFilter::from_xml(pugi::xml_node node)
     set_mesh(search->second);
   } else{
     std::stringstream err_msg;
-    err_msg << "Could not find cell " << id << " specified on tally filter.";
+    err_msg << "Could not find mesh " << id << " specified on tally filter.";
     fatal_error(err_msg);
   }
 }
@@ -37,7 +37,6 @@ const
   if (estimator != ESTIMATOR_TRACKLENGTH) {
     auto bin = model::meshes[mesh_]->get_bin(p->coord[0].xyz);
     if (bin >= 0) {
-      //TODO: off-by-one
       match.bins_.push_back(bin);
       match.weights_.push_back(1.0);
     }
diff --git a/src/tallies/filter_meshsurface.cpp b/src/tallies/filter_meshsurface.cpp
index a8854c7eca..57f10b09c3 100644
--- a/src/tallies/filter_meshsurface.cpp
+++ b/src/tallies/filter_meshsurface.cpp
@@ -22,9 +22,8 @@ MeshSurfaceFilter::text_label(int bin) const
   int n_dim = mesh.n_dimension_;
 
   // Get flattend mesh index and surface index.
-  //TODO: off-by-one
-  int i_mesh = (bin - 1) / (4 * n_dim) + 1;
-  int i_surf = ((bin - 1) % (4 * n_dim)) + 1;
+  int i_mesh = bin / (4 * n_dim);
+  int i_surf = (bin % (4 * n_dim)) + 1;
 
   // Get mesh index part of label.
   std::string out = MeshFilter::text_label(i_mesh);
diff --git a/src/tallies/filter_mu.cpp b/src/tallies/filter_mu.cpp
index 521deefe3d..78a648e239 100644
--- a/src/tallies/filter_mu.cpp
+++ b/src/tallies/filter_mu.cpp
@@ -39,8 +39,7 @@ MuFilter::get_all_bins(const Particle* p, int estimator, FilterMatch& match)
 const
 {
   if (p->mu >= bins_.front() && p->mu <= bins_.back()) {
-    //TODO: off-by-one
-    auto bin = lower_bound_index(bins_.begin(), bins_.end(), p->mu) + 1;
+    auto bin = lower_bound_index(bins_.begin(), bins_.end(), p->mu);
     match.bins_.push_back(bin);
     match.weights_.push_back(1.0);
   }
@@ -57,8 +56,7 @@ std::string
 MuFilter::text_label(int bin) const
 {
   std::stringstream out;
-  //TODO: off-by-one
-  out << "Change-in-Angle [" << bins_[bin-1] << ", " << bins_[bin] << ")";
+  out << "Change-in-Angle [" << bins_[bin] << ", " << bins_[bin+1] << ")";
   return out.str();
 }
 
diff --git a/src/tallies/filter_particle.cpp b/src/tallies/filter_particle.cpp
index 403ef9500f..967febc067 100644
--- a/src/tallies/filter_particle.cpp
+++ b/src/tallies/filter_particle.cpp
@@ -18,8 +18,7 @@ ParticleFilter::get_all_bins(const Particle* p, int estimator,
 {
   for (auto i = 0; i < particles_.size(); i++) {
     if (particles_[i] == p->type) {
-      //TODO: off-by-one
-      match.bins_.push_back(i + 1);
+      match.bins_.push_back(i);
       match.weights_.push_back(1.0);
     }
   }
diff --git a/src/tallies/filter_polar.cpp b/src/tallies/filter_polar.cpp
index 50fc47999c..5216511a9d 100644
--- a/src/tallies/filter_polar.cpp
+++ b/src/tallies/filter_polar.cpp
@@ -47,8 +47,7 @@ const
   }
 
   if (theta >= bins_.front() && theta <= bins_.back()) {
-    //TODO: off-by-one
-    auto bin = lower_bound_index(bins_.begin(), bins_.end(), theta) + 1;
+    auto bin = lower_bound_index(bins_.begin(), bins_.end(), theta);
     match.bins_.push_back(bin);
     match.weights_.push_back(1.0);
   }
@@ -65,8 +64,7 @@ std::string
 PolarFilter::text_label(int bin) const
 {
   std::stringstream out;
-  //TODO: off-by-one
-  out << "Polar Angle [" << bins_[bin-1] << ", " << bins_[bin] << ")";
+  out << "Polar Angle [" << bins_[bin] << ", " << bins_[bin+1] << ")";
   return out.str();
 }
 
diff --git a/src/tallies/filter_sph_harm.cpp b/src/tallies/filter_sph_harm.cpp
index d75be0f9d9..253bf7ff3c 100644
--- a/src/tallies/filter_sph_harm.cpp
+++ b/src/tallies/filter_sph_harm.cpp
@@ -54,8 +54,8 @@ SphericalHarmonicsFilter::get_all_bins(const Particle* p, int estimator,
     // Append the matching (bin,weight) for each moment
     for (int i = 0; i < num_nm; i++) {
       match.weights_.push_back(wgt[n] * rn[j]);
-      //TODO: off-by-one
-      match.bins_.push_back(++j);
+      match.bins_.push_back(j);
+      ++j;
     }
   }
 }
@@ -77,9 +77,8 @@ SphericalHarmonicsFilter::text_label(int bin) const
 {
   std::stringstream out;
   for (int n = 0; n < order_ + 1; n++) {
-    if (bin <= (n + 1) * (n + 1)) {
-      //TODO: off-by-one
-      int m = (bin - n*n - 1) - n;
+    if (bin < (n + 1) * (n + 1)) {
+      int m = (bin - n*n) - n;
       out << "Spherical harmonic expansion, Y" << n << "," << m;
       return out.str();
     }
diff --git a/src/tallies/filter_sptl_legendre.cpp b/src/tallies/filter_sptl_legendre.cpp
index b5d75f4d24..dae62d1d24 100644
--- a/src/tallies/filter_sptl_legendre.cpp
+++ b/src/tallies/filter_sptl_legendre.cpp
@@ -53,8 +53,7 @@ SpatialLegendreFilter::get_all_bins(const Particle* p, int estimator,
     double wgt[order_ + 1];
     calc_pn_c(order_, x_norm, wgt);
     for (int i = 0; i < order_ + 1; i++) {
-      //TODO: off-by-one
-      match.bins_.push_back(i + 1);
+      match.bins_.push_back(i);
       match.weights_.push_back(wgt[i]);
     }
   }
@@ -88,8 +87,7 @@ SpatialLegendreFilter::text_label(int bin) const
   } else {
     out << "z";
   }
-  //TODO: off-by-one
-  out << " axis, P" << std::to_string(bin - 1);
+  out << " axis, P" << std::to_string(bin);
   return out.str();
 }
 
diff --git a/src/tallies/filter_surface.cpp b/src/tallies/filter_surface.cpp
index 5b175ca708..774571d755 100644
--- a/src/tallies/filter_surface.cpp
+++ b/src/tallies/filter_surface.cpp
@@ -43,8 +43,7 @@ SurfaceFilter::get_all_bins(const Particle* p, int estimator,
 {
   auto search = map_.find(std::abs(p->surface)-1);
   if (search != map_.end()) {
-    //TODO: off-by-one
-    match.bins_.push_back(search->second + 1);
+    match.bins_.push_back(search->second);
     if (p->surface < 0) {
       match.weights_.push_back(-1.0);
     } else {
@@ -65,8 +64,7 @@ SurfaceFilter::to_statepoint(hid_t filter_group) const
 std::string
 SurfaceFilter::text_label(int bin) const
 {
-  //TODO: off-by-one
-  return "Surface " + std::to_string(model::surfaces[surfaces_[bin-1]]->id_);
+  return "Surface " + std::to_string(model::surfaces[surfaces_[bin]]->id_);
 }
 
 } // namespace openmc
diff --git a/src/tallies/filter_universe.cpp b/src/tallies/filter_universe.cpp
index ecd12b237b..5a6d5e1eba 100644
--- a/src/tallies/filter_universe.cpp
+++ b/src/tallies/filter_universe.cpp
@@ -44,8 +44,7 @@ UniverseFilter::get_all_bins(const Particle* p, int estimator,
   for (int i = 0; i < p->n_coord; i++) {
     auto search = map_.find(p->coord[i].universe);
     if (search != map_.end()) {
-      //TODO: off-by-one
-      match.bins_.push_back(search->second + 1);
+      match.bins_.push_back(search->second);
       match.weights_.push_back(1.0);
     }
   }
@@ -63,8 +62,7 @@ UniverseFilter::to_statepoint(hid_t filter_group) const
 std::string
 UniverseFilter::text_label(int bin) const
 {
-  //TODO: off-by-one
-  return "Universe " + std::to_string(model::universes[universes_[bin-1]]->id_);
+  return "Universe " + std::to_string(model::universes[universes_[bin]]->id_);
 }
 
 } // namespace openmc
diff --git a/src/tallies/filter_zernike.cpp b/src/tallies/filter_zernike.cpp
index 3ea4492388..a005f7ddcb 100644
--- a/src/tallies/filter_zernike.cpp
+++ b/src/tallies/filter_zernike.cpp
@@ -39,8 +39,7 @@ ZernikeFilter::get_all_bins(const Particle* p, int estimator,
     double zn[n_bins_];
     calc_zn(order_, r, theta, zn);
     for (int i = 0; i < n_bins_; i++) {
-      //TODO: off-by-one
-      match.bins_.push_back(i+1);
+      match.bins_.push_back(i);
       match.weights_.push_back(zn[i]);
     }
   }
@@ -62,9 +61,8 @@ ZernikeFilter::text_label(int bin) const
   std::stringstream out;
   for (int n = 0; n < order_+1; n++) {
     int last = (n + 1) * (n + 2) / 2;
-    //TODO: off-by-one
-    if (bin <= last) {
-      int first = last - n;
+    if (bin < last) {
+      int first = last - (n + 1);
       int m = -n + (bin - first) * 2;
       out << "Zernike expansion, Z" << n << "," << m;
       return out.str();
@@ -97,8 +95,7 @@ ZernikeRadialFilter::get_all_bins(const Particle* p, int estimator,
     double zn[n_bins_];
     calc_zn_rad(order_, r, zn);
     for (int i = 0; i < n_bins_; i++) {
-      //TODO: off-by-one
-      match.bins_.push_back(i+1);
+      match.bins_.push_back(i);
       match.weights_.push_back(zn[i]);
     }
   }
@@ -107,8 +104,7 @@ ZernikeRadialFilter::get_all_bins(const Particle* p, int estimator,
 std::string
 ZernikeRadialFilter::text_label(int bin) const
 {
-  //TODO: off-by-one
-  return "Zernike expansion, Z" + std::to_string(2*(bin-1)) + ",0";
+  return "Zernike expansion, Z" + std::to_string(2*bin) + ",0";
 }
 
 void
diff --git a/src/tallies/tally_scoring.cpp b/src/tallies/tally_scoring.cpp
index 96aa1abaa3..5882d241a1 100644
--- a/src/tallies/tally_scoring.cpp
+++ b/src/tallies/tally_scoring.cpp
@@ -49,7 +49,7 @@ FilterBinIter::FilterBinIter(const Tally& tally, const Particle* p)
   }
 
   // Compute the initial index and weight.
-  compute_index_weight();
+  this->compute_index_weight();
 }
 
 FilterBinIter::FilterBinIter(const Tally& tally, bool end)
@@ -67,8 +67,7 @@ FilterBinIter::FilterBinIter(const Tally& tally, bool end)
       match.bins_.clear();
       match.weights_.clear();
       for (auto i = 0; i < model::tally_filters[i_filt]->n_bins_; ++i) {
-        // TODO: off-by-one
-        match.bins_.push_back(i+1);
+        match.bins_.push_back(i);
         match.weights_.push_back(1.0);
       }
       match.bins_present_ = true;
@@ -83,7 +82,7 @@ FilterBinIter::FilterBinIter(const Tally& tally, bool end)
   }
 
   // Compute the initial index and weight.
-  compute_index_weight();
+  this->compute_index_weight();
 }
 
 FilterBinIter&
@@ -124,14 +123,13 @@ FilterBinIter::operator++()
 void
 FilterBinIter::compute_index_weight()
 {
-  index_ = 1;
+  index_ = 0;
   weight_ = 1.;
   for (auto i = 0; i < tally_.filters().size(); ++i) {
     auto i_filt = tally_.filters(i);
     auto& match {simulation::filter_matches[i_filt]};
     auto i_bin = match.i_bin_;
-    //TODO: off-by-one
-    index_ += (match.bins_[i_bin] - 1) * tally_.strides(i);
+    index_ += match.bins_[i_bin] * tally_.strides(i);
     weight_ *= match.weights_[i_bin];
   }
 }
@@ -154,19 +152,17 @@ score_fission_delayed_dg(int i_tally, int d_bin, double score, int score_index)
   dg_match.bins_[i_bin] = d_bin;
 
   // Determine the filter scoring index
-  auto filter_index = 1;
+  auto filter_index = 0;
   for (auto i = 0; i < tally.filters().size(); ++i) {
     auto i_filt = tally.filters(i);
     auto& match {simulation::filter_matches[i_filt]};
     auto i_bin = match.i_bin_;
-    //TODO: off-by-one
-    filter_index += (match.bins_[i_bin] - 1) * tally.strides(i);
+    filter_index += match.bins_[i_bin] * tally.strides(i);
   }
 
   // Update the tally result
-  // TODO: off-by-one
   #pragma omp atomic
-  tally.results_(filter_index-1, score_index, RESULT_VALUE) += score;
+  tally.results_(filter_index, score_index, RESULT_VALUE) += score;
 
   // Reset the original delayed group bin
   dg_match.bins_[i_bin] = original_bin;
@@ -217,7 +213,7 @@ score_fission_eout(const Particle* p, int i_tally, int i_score, int score_bin)
 
       // modify the value so that g_out = 1 corresponds to the highest energy
       // bin
-      g_out = eo_filt.n_bins_ - g_out + 1;
+      g_out = eo_filt.n_bins_ - g_out;
 
       // change outgoing energy bin
       simulation::filter_matches[i_eout_filt].bins_[i_bin] = g_out;
@@ -235,9 +231,8 @@ score_fission_eout(const Particle* p, int i_tally, int i_score, int score_bin)
       if (E_out < eo_filt.bins_.front() || E_out > eo_filt.bins_.back()) {
         continue;
       } else {
-        //TODO: off-by-one
         auto i_match = lower_bound_index(eo_filt.bins_.begin(),
-          eo_filt.bins_.end(), E_out) + 1;
+          eo_filt.bins_.end(), E_out);
         simulation::filter_matches[i_eout_filt].bins_[i_bin] = i_match;
       }
 
@@ -249,17 +244,17 @@ score_fission_eout(const Particle* p, int i_tally, int i_score, int score_bin)
 
       // Find the filter scoring index for this filter combination
       //TODO: should this include a weight?
-      int filter_index = 1;
+      int filter_index = 0;
       for (auto j = 0; j < tally.filters().size(); ++j) {
         auto i_filt = tally.filters(j);
         auto& match {simulation::filter_matches[i_filt]};
         auto i_bin = match.i_bin_;
-        filter_index += (match.bins_[i_bin] - 1) * tally.strides(j);
+        filter_index += match.bins_[i_bin] * tally.strides(j);
       }
 
       // Update tally results
       #pragma omp atomic
-      tally.results_(filter_index-1, i_score, RESULT_VALUE) += score;
+      tally.results_(filter_index, i_score, RESULT_VALUE) += score;
 
     } else if (score_bin == SCORE_DELAYED_NU_FISSION && g != 0) {
 
@@ -276,17 +271,15 @@ score_fission_eout(const Particle* p, int i_tally, int i_score, int score_bin)
         for (auto d_bin = 0; d_bin < dg_filt.n_bins_; ++d_bin) {
           if (dg_filt.groups_[d_bin] == g) {
             // Find the filter index and weight for this filter combination
-            int filter_index = 1;
             double filter_weight = 1.;
             for (auto j = 0; j < tally.filters().size(); ++j) {
               auto i_filt = tally.filters(j);
               auto& match {simulation::filter_matches[i_filt]};
               auto i_bin = match.i_bin_;
-              filter_index += (match.bins_[i_bin] - 1) * tally.strides(j);
               filter_weight *= match.weights_[i_bin];
             }
 
-            score_fission_delayed_dg(i_tally, d_bin+1, score*filter_weight,
+            score_fission_delayed_dg(i_tally, d_bin, score*filter_weight,
               i_score);
           }
         }
@@ -295,19 +288,19 @@ score_fission_eout(const Particle* p, int i_tally, int i_score, int score_bin)
       } else {
 
         // Find the filter index and weight for this filter combination
-        int filter_index = 1;
+        int filter_index = 0;
         double filter_weight = 1.;
         for (auto j = 0; j < tally.filters().size(); ++j) {
           auto i_filt = tally.filters(j);
           auto& match {simulation::filter_matches[i_filt]};
           auto i_bin = match.i_bin_;
-          filter_index += (match.bins_[i_bin] - 1) * tally.strides(j);
+          filter_index += match.bins_[i_bin] * tally.strides(j);
           filter_weight *= match.weights_[i_bin];
         }
 
         // Update tally results
         #pragma omp atomic
-        tally.results_(filter_index-1, i_score, RESULT_VALUE) += score*filter_weight;
+        tally.results_(filter_index, i_score, RESULT_VALUE) += score*filter_weight;
       }
     }
   }
@@ -642,7 +635,7 @@ score_general_ce(const Particle* p, int i_tally, int start_index,
                 score = p->absorb_wgt * yield
                   * simulation::micro_xs[p->event_nuclide].fission
                   / simulation::micro_xs[p->event_nuclide].absorption * flux;
-                score_fission_delayed_dg(i_tally, d_bin+1, score,
+                score_fission_delayed_dg(i_tally, d_bin, score,
                   score_index);
               }
               continue;
@@ -677,7 +670,7 @@ score_general_ce(const Particle* p, int i_tally, int start_index,
               auto d = filt.groups_[d_bin];
               score = simulation::keff * p->wgt_bank / p->n_bank
                 * p->n_delayed_bank[d-1] * flux;
-              score_fission_delayed_dg(i_tally, d_bin+1, score, score_index);
+              score_fission_delayed_dg(i_tally, d_bin, score, score_index);
             }
             continue;
           } else {
@@ -702,7 +695,7 @@ score_general_ce(const Particle* p, int i_tally, int start_index,
                 ->nu(E, ReactionProduct::EmissionMode::delayed, d);
               score = simulation::micro_xs[i_nuclide].fission * yield
                 * atom_density * flux;
-              score_fission_delayed_dg(i_tally, d_bin+1, score, score_index);
+              score_fission_delayed_dg(i_tally, d_bin, score, score_index);
             }
             continue;
           } else {
@@ -731,7 +724,7 @@ score_general_ce(const Particle* p, int i_tally, int start_index,
                     ->nu(E, ReactionProduct::EmissionMode::delayed, d);
                   score = simulation::micro_xs[j_nuclide].fission * yield
                     * atom_density * flux;
-                  score_fission_delayed_dg(i_tally, d_bin+1, score,
+                  score_fission_delayed_dg(i_tally, d_bin, score,
                     score_index);
                 }
               }
@@ -782,7 +775,7 @@ score_general_ce(const Particle* p, int i_tally, int start_index,
                   * simulation::micro_xs[p->event_nuclide].fission
                   / simulation::micro_xs[p->event_nuclide].absorption
                   * rate * flux;
-                score_fission_delayed_dg(i_tally, d_bin+1, score,
+                score_fission_delayed_dg(i_tally, d_bin, score,
                   score_index);
               }
               continue;
@@ -836,7 +829,7 @@ score_general_ce(const Particle* p, int i_tally, int start_index,
                 for (auto d_bin = 0; d_bin < filt.n_bins_; ++d_bin) {
                   auto d = filt.groups_[d_bin];
                   if (d == g)
-                    score_fission_delayed_dg(i_tally, d_bin+1, score,
+                    score_fission_delayed_dg(i_tally, d_bin, score,
                       score_index);
                 }
                 score = 0.;
@@ -862,7 +855,7 @@ score_general_ce(const Particle* p, int i_tally, int start_index,
               auto rate = rxn.products_[d].decay_rate_;
               score = simulation::micro_xs[i_nuclide].fission * yield * flux
                 * atom_density * rate;
-              score_fission_delayed_dg(i_tally, d_bin+1, score, score_index);
+              score_fission_delayed_dg(i_tally, d_bin, score, score_index);
             }
             continue;
           } else {
@@ -902,7 +895,7 @@ score_general_ce(const Particle* p, int i_tally, int start_index,
                     auto rate = rxn.products_[d].decay_rate_;
                     score = simulation::micro_xs[j_nuclide].fission * yield
                       * flux * atom_density * rate;
-                    score_fission_delayed_dg(i_tally, d_bin+1, score,
+                    score_fission_delayed_dg(i_tally, d_bin, score,
                       score_index);
                   }
                 }
@@ -1214,7 +1207,7 @@ score_general_ce(const Particle* p, int i_tally, int start_index,
 
     // Update tally results
     #pragma omp atomic
-    tally.results_(filter_index-1, score_index, RESULT_VALUE) += score;
+    tally.results_(filter_index, score_index, RESULT_VALUE) += score;
   }
 }
 
@@ -1229,8 +1222,6 @@ score_general_mg(const Particle* p, int i_tally, int start_index,
 {
   auto& tally {*model::tallies[i_tally]};
 
-  //TODO: off-by-one throughout on p->material
-
   // Set the direction and group to use with get_xs
   const double* p_uvw;
   int p_g;
@@ -1626,7 +1617,7 @@ score_general_mg(const Particle* p, int i_tally, int start_index,
                       p_g, nullptr, nullptr, &d)
                     / get_macro_xs(p->material, MG_GET_XS_ABSORPTION, p_g);
                 }
-                score_fission_delayed_dg(i_tally, d_bin+1, score,
+                score_fission_delayed_dg(i_tally, d_bin, score,
                   score_index);
               }
               continue;
@@ -1671,7 +1662,7 @@ score_general_mg(const Particle* p, int i_tally, int start_index,
                   * get_nuclide_xs(i_nuclide+1, MG_GET_XS_FISSION, p_g)
                   / get_macro_xs(p->material, MG_GET_XS_FISSION, p_g);
               }
-              score_fission_delayed_dg(i_tally, d_bin+1, score, score_index);
+              score_fission_delayed_dg(i_tally, d_bin, score, score_index);
             }
             continue;
           } else {
@@ -1705,7 +1696,7 @@ score_general_mg(const Particle* p, int i_tally, int start_index,
                 * get_macro_xs(p->material, MG_GET_XS_DELAYED_NU_FISSION,
                                p_g, nullptr, nullptr, &d);
             }
-            score_fission_delayed_dg(i_tally, d_bin+1, score, score_index);
+            score_fission_delayed_dg(i_tally, d_bin, score, score_index);
           }
           continue;
         } else {
@@ -1752,7 +1743,7 @@ score_general_mg(const Particle* p, int i_tally, int start_index,
                                    p_g, nullptr, nullptr, &d)
                     / get_macro_xs(p->material, MG_GET_XS_ABSORPTION, p_g);
                 }
-                score_fission_delayed_dg(i_tally, d_bin+1, score,
+                score_fission_delayed_dg(i_tally, d_bin, score,
                   score_index);
               }
               continue;
@@ -1817,7 +1808,7 @@ score_general_mg(const Particle* p, int i_tally, int start_index,
                 for (auto d_bin = 0; d_bin < filt.n_bins_; ++d_bin) {
                   auto d = filt.groups_[d_bin];
                   if (d == g)
-                    score_fission_delayed_dg(i_tally, d_bin+1, score,
+                    score_fission_delayed_dg(i_tally, d_bin, score,
                       score_index);
                 }
                 score = 0.;
@@ -1848,7 +1839,7 @@ score_general_mg(const Particle* p, int i_tally, int start_index,
                 * get_macro_xs(p->material, MG_GET_XS_DELAYED_NU_FISSION,
                                p_g, nullptr, nullptr, &d);
             }
-            score_fission_delayed_dg(i_tally, d_bin+1, score, score_index);
+            score_fission_delayed_dg(i_tally, d_bin, score, score_index);
           }
           continue;
         } else {
@@ -1921,7 +1912,7 @@ score_general_mg(const Particle* p, int i_tally, int start_index,
 
     // Update tally results
     #pragma omp atomic
-    tally.results_(filter_index-1, score_index, RESULT_VALUE) += score;
+    tally.results_(filter_index, score_index, RESULT_VALUE) += score;
   }
 }
 
@@ -2044,12 +2035,8 @@ void score_analog_tally_mg(const Particle* p)
 
         double atom_density = 0.;
         if (i_nuclide >= 0) {
-          //TODO: off-by-one
-          auto j = model::materials[p->material]
-            ->mat_nuclide_index_[i_nuclide];
+          auto j = model::materials[p->material]->mat_nuclide_index_[i_nuclide];
           if (j == C_NONE) continue;
-          //atom_density = material_atom_density(p->material, j);
-          //TODO: off-by-one
           atom_density = model::materials[p->material]->atom_density_(j);
         }
 
@@ -2103,12 +2090,8 @@ score_tracklength_tally(const Particle* p, double distance)
           double atom_density = 0.;
           if (i_nuclide >= 0) {
             if (p->material != MATERIAL_VOID) {
-              //TODO: off-by-one
-              auto j = model::materials[p->material]
-                ->mat_nuclide_index_[i_nuclide];
+              auto j = model::materials[p->material]->mat_nuclide_index_[i_nuclide];
               if (j == C_NONE) continue;
-              //atom_density = material_atom_density(p->material, j);
-              //TODO: off-by-one
               atom_density = model::materials[p->material]->atom_density_(j);
             }
           }
@@ -2173,12 +2156,8 @@ void score_collision_tally(const Particle* p)
 
           double atom_density = 0.;
           if (i_nuclide >= 0) {
-            //TODO: off-by-one
-            auto j = model::materials[p->material]
-              ->mat_nuclide_index_[i_nuclide];
+            auto j = model::materials[p->material]->mat_nuclide_index_[i_nuclide];
             if (j == C_NONE) continue;
-            //atom_density = material_atom_density(p->material, j);
-            //TODO: off-by-one
             atom_density = model::materials[p->material]->atom_density_(j);
           }
 
@@ -2233,9 +2212,8 @@ score_surface_tally(const Particle* p, const std::vector<int>& tallies)
       double score = flux * filter_weight;
       for (auto score_index = 0; score_index < tally.scores_.size();
            ++score_index) {
-        //TODO: off-by-one
         #pragma omp atomic
-        tally.results_(filter_index-1, score_index, RESULT_VALUE) += score;
+        tally.results_(filter_index, score_index, RESULT_VALUE) += score;
       }
     }