def _get_and_count_containers(self, custom_cgroups=False, healthchecks=False):
        """List all the containers from the API, filter and count them."""

        # Querying the size of containers is slow, we don't do it at each run
        must_query_size = self.collect_container_size and self._latest_size_query == 0
        self._latest_size_query = (self._latest_size_query + 1) % SIZE_REFRESH_RATE

        running_containers_count = Counter()
        all_containers_count = Counter()

        try:
            containers = self.docker_util.client.containers(all=True, size=must_query_size)
        except Exception as e:
            message = "Unable to list Docker containers: {0}".format(e)
            self.service_check(SERVICE_CHECK_NAME, AgentCheck.CRITICAL,
                               message=message, tags=self.custom_tags)
            raise Exception(message)

        else:
            self.service_check(SERVICE_CHECK_NAME, AgentCheck.OK, tags=self.custom_tags)

        # Create a set of filtered containers based on the exclude/include rules
        # and cache these rules in docker_util
        self._filter_containers(containers)

        containers_by_id = {}

        for container in containers:
            container_name = DockerUtil.container_name_extractor(container)[0]

            container_status_tags = self._get_tags(container, CONTAINER)

            all_containers_count[tuple(sorted(container_status_tags))] += 1
            if self._is_container_running(container):
                running_containers_count[tuple(sorted(container_status_tags))] += 1

            # Check if the container is included/excluded via its tags
            if self._is_container_excluded(container):
                self.log.debug("Container {0} is excluded".format(container_name))
                continue

            containers_by_id[container['Id']] = container

            # grab pid via API if custom cgroups - otherwise we won't find process when
            # crawling for pids.
            if custom_cgroups or healthchecks:
                try:
                    inspect_dict = self.docker_util.client.inspect_container(container_name)
                    container['_pid'] = inspect_dict['State']['Pid']
                    container['health'] = inspect_dict['State'].get('Health', {})
                except Exception as e:
                    self.log.debug("Unable to inspect Docker container: %s", e)

        total_count = 0
        # TODO: deprecate these 2, they should be replaced by _report_container_count
        for tags, count in running_containers_count.iteritems():
            total_count += count
            self.gauge("docker.containers.running", count, tags=list(tags))
        self.gauge("docker.containers.running.total", total_count, tags=self.custom_tags)

        total_count = 0
        for tags, count in all_containers_count.iteritems():
            stopped_count = count - running_containers_count[tags]
            total_count += stopped_count
            self.gauge("docker.containers.stopped", stopped_count, tags=list(tags))
        self.gauge("docker.containers.stopped.total", total_count, tags=self.custom_tags)

        return containers_by_id