meteor__microscope/client/templates/notifications/notifications.js

Template.notifications.helpers({
  notifications: function () {
    return Notifications.find({
      userId: Meteor.userId(),
      read: false
    });
  },

  notificationCount: function () {
    return Notifications.find({
      userId: Meteor.userId(),
      read: false
    }).count();
  }
});

Template.notificationItem.helpers({
  notificationPostPath: function () {
    return Router.routes.postPage.path({ _id: this.postId });
  }
});

Template.notificationItem.events({
  'click a': function () {
    // Here, "this" is a Notification document..
    Notifications.update(this._id, { $set : { read: true }});
  }
});